4MLG

Structure of RS223-Beta-xylosidase

PDB DOI: https://doi.org/10.2210/pdb4MLG/pdb

Classification: HYDROLASE
Organism(s): uncultured organism
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-06 Released: 2014-09-17
Deposition Author(s): Jordan, D., Braker, J., Wagschal, K., Lee, C., Dubrovska, I., Anderson, S., Wawrzak, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.257
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of RS223-Beta-xylosidase

Jordan, D., Braker, J., Wagschal, K., Lee, C., Dubrovska, I., Anderson, S., Wawrzak, Z.

To be published.

Macromolecule Content

Total Structure Weight: 453.33 kDa
Atom Count: 32,402
Modelled Residue Count: 3,875
Deposited Residue Count: 3,888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	324	uncultured organism	Mutation(s): 0 Gene Names: rs223-bx EC: 3.2.1.37
UniProt
Find proteins for I7EUE2 (uncultured organism) Explore I7EUE2 Go to UniProtKB: I7EUE2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7EUE2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain LA [auth I] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth J] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth K] SDF format, chain SA [auth K] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth L] mmCIF format, chain VA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], MA [auth I], N [auth A], O [auth A], OA [auth J], PA [auth J], Q [auth B], R [auth B], RA [auth K], SA [auth K], T [auth C], U [auth C], UA [auth L], VA [auth L], W [auth D], X [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain KA [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth J] SDF format, chain P [auth B] SDF format, chain QA [auth K] SDF format, chain S [auth C] SDF format, chain TA [auth L] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain TA [auth L] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] BA [auth F], EA [auth G], HA [auth H], KA [auth I], M [auth A], NA [auth J], P [auth B], QA [auth K], S [auth C], TA [auth L], V [auth D], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.257
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.525	α = 90
b = 148.702	β = 112.87
c = 125.648	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary