3QXB

Crystal structure of a Putative Xylose isomerase (YP_426450.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QXB/pdb

Classification: ISOMERASE
Organism(s): Rhodospirillum rubrum ATCC 11170
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-01 Released: 2011-03-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.150 (Depositor), 0.170 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a Putative Xylose isomerase (YP_426450.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 147.93 kDa
Atom Count: 10,645
Modelled Residue Count: 1,185
Deposited Residue Count: 1,264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Xylose isomerase	A, B, C, D	316	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Gene Names: Rru_A1362
UniProt
Find proteins for Q2RUN2 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RUN2 Go to UniProtKB: Q2RUN2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RUN2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	EA [auth C] FA [auth C] GA [auth C] K [auth A] L [auth A] EA [auth C], FA [auth C], GA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth D], O [auth A], OA [auth D], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Y [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Y [auth B]	HA [auth C], P [auth A], PA [auth D], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain HA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth C] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Y [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	CA [auth C] E [auth A] H [auth A] IA [auth D] LA [auth D] CA [auth C], E [auth A], H [auth A], IA [auth D], LA [auth D], Q [auth B], T [auth B], Z [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain E [auth A] Focus chain H [auth A] Focus chain IA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth C] Focus chain E [auth A] Focus chain H [auth A] Focus chain IA [auth D] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain T [auth B] Focus chain Z [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	AA [auth C] BA [auth C] F [auth A] G [auth A] JA [auth D] AA [auth C], BA [auth C], F [auth A], G [auth A], JA [auth D], KA [auth D], R [auth B], S [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth D] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain U [auth B]	DA [auth C], I [auth A], J [auth A], MA [auth D], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth D] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain MA [auth D] Focus chain U [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.150 (Depositor), 0.170 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33QXB

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.188	α = 90
b = 94.903	β = 93.04
c = 173.197	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Refinement description, Structure summary