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- PDB-2d7v: Structure of OsmC-like Protein of Unknown Function VCA0330 from V... -

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Basic information

Entry
Database: PDB / ID: 2d7v
TitleStructure of OsmC-like Protein of Unknown Function VCA0330 from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsHypothetical protein VCA0330
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Vibrio cholerae / hypothetial protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / OsmC/Ohr family protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsBinkowski, T.A. / Hatzos, C. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Hypothetical protein VCA0330 from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Binkowski, T.A. / Hatzos, C. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionNov 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein VCA0330
B: Hypothetical protein VCA0330


Theoretical massNumber of molelcules
Total (without water)35,7752
Polymers35,7752
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-53 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.507, 40.023, 56.231
Angle α, β, γ (deg.)90.00, 108.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein VCA0330


Mass: 17887.662 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: VCA0330 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 9657729, UniProt: Q9KMK9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.0M (NH4)2HPO4, 0.1M Acetate pH 4.5, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 24581 / Num. obs: 23797 / % possible obs: 76.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.97→2.07 Å / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.335 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.166 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25846 1248 5.1 %RANDOM
Rwork0.19925 ---
obs0.20218 23328 76.62 %-
all-24581 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.06 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 0 88 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9363308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4715307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88624.851101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.259158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21107
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21692
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1471.51578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86822509
X-RAY DIFFRACTIONr_scbond_it3.0113953
X-RAY DIFFRACTIONr_scangle_it4.8864.5799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 1.97 Å / Num. reflection Rwork: 119 / Total num. of bins used: 20

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