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- PDB-1u9d: Structure of Protein of Unknown Function from Vibrio cholerae O1 ... -

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Basic information

Entry
Database: PDB / ID: 1u9d
TitleStructure of Protein of Unknown Function from Vibrio cholerae O1 biovar eltor str. N16961
Componentshypothetical protein VC0714
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / hypothetical protein / protein structure initiative / PSI / Midwest Center for Structural Genomics
Function / homologyProtein of unknown function DUF1904 / Domain of unknown function (DUF1904) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / DUF1904 domain-containing protein
Function and homology information
Biological speciesVibrio cholerae O1 biovar eltor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsBinkowski, T.A. / Wu, R. / Moy, S.F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Hypothetical Protein from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Binkowski, T.A. / Wu, R. / Moy, S.F. / Joachimiak, A.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS SEE A DIMER IN THE ASYMMETRIC UNIT BUT ARE UNSURE OF THE BIOLOGICAL ACTIVITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein VC0714
B: hypothetical protein VC0714
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0054
Polymers27,8152
Non-polymers1902
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein VC0714
hetero molecules

A: hypothetical protein VC0714
hetero molecules

A: hypothetical protein VC0714
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0076
Polymers41,7223
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6380 Å2
ΔGint-33 kcal/mol
Surface area16350 Å2
MethodPISA, PQS
3
B: hypothetical protein VC0714
hetero molecules

B: hypothetical protein VC0714
hetero molecules

B: hypothetical protein VC0714
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0076
Polymers41,7223
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.006, 66.006, 47.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-263-

HOH

21B-262-

HOH

31B-263-

HOH

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Components

#1: Protein hypothetical protein VC0714


Mass: 13907.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria)
Species: Vibrio cholerae / Strain: O1 biovar eltor str. N16961 / Gene: VC0714 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9KU16
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2M NaH2P04/0.8M K2HP04, CAPS, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9796 Å
DetectorType: SBC-1 / Detector: CCD / Date: Jun 28, 2004
Details: Double crystal monochromatic, sagitally focused si(111)
RadiationMonochromator: Sagitally focused si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→56.8 Å / Num. all: 24579 / Num. obs: 23325 / % possible obs: 95.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→56.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.14 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23702 1254 5.1 %RANDOM
Rwork0.18903 ---
all0.19148 24579 --
obs0.19146 23325 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 10 153 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212004
X-RAY DIFFRACTIONr_bond_other_d0.0020.021792
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9392730
X-RAY DIFFRACTIONr_angle_other_deg0.86634138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95242
X-RAY DIFFRACTIONr_chiral_restr0.0950.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022246
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
X-RAY DIFFRACTIONr_nbd_refined0.240.2441
X-RAY DIFFRACTIONr_nbd_other0.2460.22140
X-RAY DIFFRACTIONr_nbtor_other0.0880.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.2146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.239
X-RAY DIFFRACTIONr_mcbond_it1.11.51212
X-RAY DIFFRACTIONr_mcangle_it2.20421956
X-RAY DIFFRACTIONr_scbond_it3.4753792
X-RAY DIFFRACTIONr_scangle_it5.7944.5774
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.411 62
Rwork0.359 1140

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