2Q5C | pdb_00002q5c

Crystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb2Q5C/pdb

Classification: TRANSCRIPTION
Organism(s): Clostridium acetobutylicum ATCC 824
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-05-31 Released: 2007-07-03
Deposition Author(s): Ramagopal, U.A., Dickey, M., Toro, R., Iizuka, M., Groshong, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.187 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum.

Ramagopal, U.A., Dickey, M., Toro, R., Iizuka, M., Groshong, K., Rodgers, L., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 45.29 kDa
Atom Count: 3,566
Modeled Residue Count: 374
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NtrC family transcriptional regulator	A, B [auth D]	196	Clostridium acetobutylicum ATCC 824	Mutation(s): 0 Gene Names: CA_C0459
UniProt
Find proteins for Q97LU5 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97LU5 Go to UniProtKB: Q97LU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97LU5
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 C [auth A] 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 J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain C [auth A] 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 J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain C [auth A] 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 J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth D], K [auth D], L [auth D], M [auth D], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	H [auth A], I [auth A], P [auth D], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.187 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.95	α = 72.94
b = 45.948	β = 72.98
c = 58.284	γ = 82.07

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-02-21
Changes: Data collection, Database references