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- PDB-1y9b: Structure of Conserved Putative Transcriptional Factor from Vibri... -

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Basic information

Entry
Database: PDB / ID: 1y9b
TitleStructure of Conserved Putative Transcriptional Factor from Vibrio cholerae O1 biovar eltor str. N16961
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Vibrio cholerae / conserved hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
VCA0319-like / Single helix bin / Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / cAMP-dependent Protein Kinase, Chain A / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...VCA0319-like / Single helix bin / Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / cAMP-dependent Protein Kinase, Chain A / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF1778 domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBinkowski, T.A. / Hatzos, C. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Conserverd hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Binkowski, T.A. / Hatzos, C. / Quartey, P. / Moy, S. / Joachimiak, A.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)19,5762
Polymers19,5762
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-26 kcal/mol
Surface area11420 Å2
MethodPISA
2
A: conserved hypothetical protein

A: conserved hypothetical protein

B: conserved hypothetical protein

B: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)39,1524
Polymers39,1524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_656-x+1,-y,z+11
Buried area3580 Å2
ΔGint-43 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.220, 72.732, 48.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein conserved hypothetical protein


Mass: 9787.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Species: Vibrio cholerae / Strain: N16961 / Gene: VCA0319 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2J6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 1.1M Sodium malonate, 0.1M Hepes, 0.5% w/v jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97944 Å
DetectorType: SBC-2 / Detector: CCD / Date: Oct 11, 2004 / Details: sagitally focused SI(111)
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.2→48.97 Å / Num. all: 22383 / Num. obs: 12046 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.97 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.828 / SU B: 15.305 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28598 587 4.9 %RANDOM
Rwork0.22453 ---
all0.22747 22383 --
obs0.22747 11459 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 123 1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221189
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9951609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06326.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68915228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.506156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02836
X-RAY DIFFRACTIONr_nbd_refined0.2090.2505
X-RAY DIFFRACTIONr_nbtor_refined0.2790.2856
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.217
X-RAY DIFFRACTIONr_mcbond_it1.4631.5820
X-RAY DIFFRACTIONr_mcangle_it1.59321273
X-RAY DIFFRACTIONr_scbond_it2.8693398
X-RAY DIFFRACTIONr_scangle_it4.9614.5335
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 35 -
Rwork0.358 819 -
obs--97.71 %

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