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- PDB-2qzj: Crystal structure of a two-component response regulator from Clos... -

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Basic information

Entry
Database: PDB / ID: 2qzj
TitleCrystal structure of a two-component response regulator from Clostridium difficile
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / 11017x / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA-binding / Phosphorylation / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage 0 sporulation protein A homolog
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a two-component response regulator from Clostridium difficile.
Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component response regulator
B: Two-component response regulator
C: Two-component response regulator
D: Two-component response regulator
E: Two-component response regulator
F: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)94,3066
Polymers94,3066
Non-polymers00
Water1,40578
1
A: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7181
Polymers15,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.044, 75.044, 314.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Two-component response regulator


Mass: 15717.610 Da / Num. of mol.: 6 / Fragment: Residues 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD3265 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q180B0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 11, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 21182 / Num. obs: 21182 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 17.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.8
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 5 / Num. unique all: 2015 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.89→48.18 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 86090.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1223 5.9 %RANDOM
Rwork0.219 ---
all0.257 ---
obs0.219 20884 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.8003 Å2 / ksol: 0.379896 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.89→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5766 0 0 78 5844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.68
LS refinement shellResolution: 2.89→3.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 198 6 %
Rwork0.261 3086 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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