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- PDB-2haf: Crystal structure of a putative translation repressor from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 2haf
TitleCrystal structure of a putative translation repressor from Vibrio cholerae
ComponentsPutative translation repressor
KeywordsTRANSLATION REPRESSOR / alpha/beta / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


VC0467-like domains / VC0467-like / VC0467-like / Protein of unknown function UPF0301 / AlgH-like / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0301 protein VC_0467
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å
AuthorsSugadev, R. / Seetharaman, J. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative translation repressor from Vibrio cholerae
Authors: Sugadev, R. / Seetharaman, J. / Kumaran, D. / Swaminathan, S.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative translation repressor


Theoretical massNumber of molelcules
Total (without water)23,4181
Polymers23,4181
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.36, 59.36, 236.74
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative translation repressor


Mass: 23418.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KUP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 1.4 M tri-sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.979
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 2, 2006mirrors
ADSC QUANTUM 3152CCDJun 2, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionResolution: 2.88→50 Å / Num. all: 6206 / Num. obs: 6206 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.09 / Net I/σ(I): 16.8
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 5.7 % / Num. unique all: 6291 / Rsym value: 0.214 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.88→34.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 168985.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed in remark 465 and atoms listed in remark 470 were not modeled due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 952 15.9 %RANDOM
Rwork0.241 ---
obs0.241 5995 96.6 %-
all-5995 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.5048 Å2 / ksol: 0.335334 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å29.8 Å20 Å2
2---2.64 Å20 Å2
3---5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.88→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 0 21 1445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.88→3.06 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 155 16.8 %
Rwork0.338 765 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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