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- PDB-4ovb: Crystal structure of Oncogenic Suppression Activity Protein - A P... -

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Basic information

Entry
Database: PDB / ID: 4ovb
TitleCrystal structure of Oncogenic Suppression Activity Protein - A Plasmid Fertility Inhibition Factor, Gold (I) Cyanide derivative
ComponentsProtein osa
KeywordsANTITUMOR PROTEIN / Plasmid Fertility Inhibition
Function / homologyFiwA/Osa / : / Plasmid Fertility inhibition factor / GOLD (I) CYANIDE ION / PHOSPHATE ION / Protein osa
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.034 Å
AuthorsMaindola, P. / Goyal, P. / Arulandu, A.
CitationJournal: Nat Commun / Year: 2014
Title: Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids
Authors: Maindola, P. / Raina, R. / Goyal, P. / Atmakuri, K. / Ojha, A. / Gupta, S. / Christie, P.J. / Iyer, L.M. / Aravind, L. / Arockiasamy, A.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein osa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,70915
Polymers21,0011
Non-polymers2,70714
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.997, 60.997, 126.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein osa


Mass: 21001.391 Da / Num. of mol.: 1 / Mutation: R4W
Source method: isolated from a genetically manipulated source
Details: IncW plasmid Sa (pSa) / Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: osa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29772
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-AUC / GOLD (I) CYANIDE ION


Mass: 249.001 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2AuN2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 10% Isopropanol, 0.5M lithium sulphate, 0.1M phosphate-citrate buffer pH 4.2, 0.2M NDSB-201, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 31, 2007 / Details: VariMax
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 16254 / Num. obs: 15539 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 46.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 61.21
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.548 / % possible all: 85.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXCDEmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.034→27.49 Å / SU ML: 0.2 / σ(F): 1.38 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 776 5 %RANDOM
Rwork0.1913 ---
all0.1934 16079 --
obs0.1934 15512 96.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.034→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 47 108 1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071542
X-RAY DIFFRACTIONf_angle_d1.1022102
X-RAY DIFFRACTIONf_dihedral_angle_d14.125549
X-RAY DIFFRACTIONf_chiral_restr0.069236
X-RAY DIFFRACTIONf_plane_restr0.005266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0344-2.16180.2821370.2457228592
2.1618-2.32860.28651170.2204237195
2.3286-2.56280.31981350.203240396
2.5628-2.93330.29091240.2048245297
2.9333-3.69420.22691250.1923251798
3.6942-27.49240.19131380.1742270899

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