1XRG

Conserved hypothetical protein from Clostridium thermocellum Cth-2968

PDB DOI: https://doi.org/10.2210/pdb1XRG/pdb

Classification: structural genomics, unknown function
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-10-14 Released: 2004-12-14
Deposition Author(s): Zhao, M., Chang, J., Habel, J., Kataeva, I., Xu, H., Chen, L., Lee, D., Nguyen, J., Chang, S.-H., Horanyi, P., Florence, Q., Zhou, W., Tempel, W., Lin, D., Zhang, H., Arendall III, W.B., Ljundahl, L., Liu, Z.-J., Rose, J., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.225
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

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

Literature

Conserved hypothetical protein from Clostridium thermocellum Cth-2968

Zhao, M., Chang, J., Habel, J., Kataeva, I., Xu, H., Chen, L., Lee, D., Nguyen, J., Chang, S.-H., Horanyi, P., Florence, Q., Zhou, W., Tempel, W., Lin, D., Zhang, H., Arendall III, W.B., Ljundahl, L., Liu, Z.-J., Rose, J., Richardson, J.S., Richardson, D.C., Wang, B.-C., Southeast Collaboratory for Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 51.11 kDa
Atom Count: 3,105
Modelled Residue Count: 400
Deposited Residue Count: 468
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 translation initiation inhibitor, yjgF family	A, B, C	156	Acetivibrio thermocellus	Mutation(s): 2
UniProt
Find proteins for A3DJ68 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DJ68 Go to UniProtKB: A3DJ68
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DJ68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] 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 O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] 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 O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] 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 O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth B], R [auth B], S [auth C], T [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.225
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.436	α = 90
b = 80.436	β = 90
c = 137.202	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ISAS	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-12-14

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2004-12-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary