3G85 | pdb_00003g85

Crystal structure of LacI family transcription regulator from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb3G85/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Clostridium acetobutylicum ATCC 824
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-11 Released: 2009-02-24
Deposition Author(s): Bagaria, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3G85

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

Literature

Crystal structure of LacI family transcription regulator from Clostridium acetobutylicum

Bagaria, A., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.71 kDa
Atom Count: 2,331
Modeled Residue Count: 270
Deposited Residue Count: 289
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator (LacI family)	A	289	Clostridium acetobutylicum ATCC 824	Mutation(s): 0 Gene Names: CA_C3553
UniProt
Find proteins for Q97DC5 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97DC5 Go to UniProtKB: Q97DC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97DC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.184 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.024	α = 90
b = 96.058	β = 90
c = 99.976	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-02-24

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-02-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.