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- PDB-3h5o: The crystal structure of transcription regulator GntR from Chromo... -

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Basic information

Entry
Database: PDB / ID: 3h5o
TitleThe crystal structure of transcription regulator GntR from Chromobacterium violaceum
ComponentsTranscriptional regulator GntR
Keywordstranscription regulator / 11234b / GntR / Chromobacterium violaceum / PSI / SGX / DNA-binding / Transcription / Transcription regulation / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator GntR
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / solve / Resolution: 2.3 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of transcription regulator GntR from Chromobacterium violaceum
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator GntR
B: Transcriptional regulator GntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9664
Polymers74,7742
Non-polymers1922
Water3,567198
1
A: Transcriptional regulator GntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4832
Polymers37,3871
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator GntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4832
Polymers37,3871
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-54 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.365, 67.882, 90.362
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator GntR


Mass: 37386.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_2956, gntR / Plasmid: BC-pSGX(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL-Stratagene / References: UniProt: Q7NTU7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v PEG 3350, 0.2 M Lithium sulfate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→90.17 Å / Num. obs: 29909 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4334 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: solve / Resolution: 2.3→90.17 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / σ(F): 1.18 / Stereochemistry target values: Engh & Huber
Details: More than 60 residues could not be modeled on the N-terminal (in both chains) due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1515 5.07 %Random
Rwork0.1892 ---
obs0.1913 29884 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL. / Bsol: 38.846 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 30.77 Å2
Baniso -1Baniso -2Baniso -3
1--6.16 Å20 Å2-5.3848 Å2
2--4.8018 Å2-0 Å2
3---1.3582 Å2
Refinement stepCycle: LAST / Resolution: 2.3→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 10 198 4334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.27681420.23172544X-RAY DIFFRACTION100
2.3742-2.45910.2351350.21112552X-RAY DIFFRACTION100
2.4591-2.55760.27511680.2072528X-RAY DIFFRACTION100
2.5576-2.6740.28911400.20392574X-RAY DIFFRACTION100
2.674-2.8150.2651160.2012614X-RAY DIFFRACTION100
2.815-2.99130.27681140.1922570X-RAY DIFFRACTION100
2.9913-3.22230.27031220.19482605X-RAY DIFFRACTION100
3.2223-3.54660.20771390.17662584X-RAY DIFFRACTION100
3.5466-4.05980.19981380.16112581X-RAY DIFFRACTION100
4.0598-5.11490.19381470.15652593X-RAY DIFFRACTION100
5.1149-90.35030.21241540.19382624X-RAY DIFFRACTION99

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