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- PDB-4o7k: Crystal structure of Oncogenic Suppression Activity Protein - A P... -

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Basic information

Entry
Database: PDB / ID: 4o7k
TitleCrystal structure of Oncogenic Suppression Activity Protein - A Plasmid Fertility Inhibition Factor
ComponentsProtein osa
KeywordsANTITUMOR PROTEIN / Plasmid Fertility Inhibition
Function / homologyFiwA/Osa / : / Plasmid Fertility inhibition factor / ISOPROPYL ALCOHOL / PHOSPHATE ION / Protein osa
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.748 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
DepositionDec 25, 2013Deposition 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: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)21,6236
Polymers21,2781
Non-polymers3465
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.869, 60.869, 126.898
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 / ONCOGENIC SUPPRESSION ACTIVITY PROTEIN


Mass: 21277.684 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
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: 1.748→50 Å / Num. all: 25018 / Num. obs: 24068 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25.8 % / Biso Wilson estimate: 28.01 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.748→1.81 Å / Rmerge(I) obs: 0.433 / % possible all: 80.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXCDEmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.748→25.537 Å / FOM work R set: 0.7847 / SU ML: 0.22 / σ(F): 1.41 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1217 5.06 %RANDOM
Rwork0.1966 ---
all0.1986 24923 --
obs0.1986 24031 96.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 35.19 Å2 / Biso min: 19.78 Å2
Refinement stepCycle: LAST / Resolution: 1.748→25.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 19 111 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061611
X-RAY DIFFRACTIONf_angle_d0.9912210
X-RAY DIFFRACTIONf_dihedral_angle_d14.768585
X-RAY DIFFRACTIONf_chiral_restr0.037241
X-RAY DIFFRACTIONf_plane_restr0.005285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7485-1.81850.3808990.33242090218981
1.8185-1.90120.3371420.29512451259395
1.9012-2.00140.29831290.2482516264597
2.0014-2.12670.29191250.22032535266098
2.1267-2.29080.26191550.19382536269198
2.2908-2.52120.26291380.19422581271999
2.5212-2.88560.24931480.19942608275699
2.8856-3.63390.22291320.195826652797100
3.6339-25.53980.18861490.169228322981100

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