1XMA

Structure of a transcriptional regulator from Clostridium thermocellum Cth-833

PDB DOI: https://doi.org/10.2210/pdb1XMA/pdb

Classification: TRANSCRIPTION
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-10-01 Released: 2004-12-14
Deposition Author(s): Yang, H., Chen, L., Lee, D., Habel, J., Nguyen, J., Chang, S.-H., Kataeva, I., Xu, H., Chang, J., Zhao, M., Horanyi, P., Florence, Q., Zhou, W., Tempel, W., Lin, D., Praissman, J., Zhang, H., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Ljungdahl, L., Liu, Z.-J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267
R-Value Work: 0.205
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of a transcriptional regulator from Clostridium thermocellum Cth-833

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

To be published.

Macromolecule Content

Total Structure Weight: 34.36 kDa
Atom Count: 1,775
Modelled Residue Count: 204
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted transcriptional regulator	A, B	145	Acetivibrio thermocellus	Mutation(s): 0
UniProt
Find proteins for A3DGR1 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DGR1 Go to UniProtKB: A3DGR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DGR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267
R-Value Work: 0.205
R-Value Observed: 0.209
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.483	α = 90
b = 52.16	β = 92.46
c = 51.076	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ISAS	phasing

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: 2008-01-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2020-03-18
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations