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- PDB-2okt: Crystal structure of O-succinylbenzoic acid synthetase from Staph... -

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Basic information

Entry
Database: PDB / ID: 2okt
TitleCrystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, ligand-free form
ComponentsO-succinylbenzoic acid synthetase
KeywordsLYASE / ENOLASE / O-SUCCINYLBENZOIC ACID SYNTHETASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / menaquinone biosynthetic process / magnesium ion binding
Similarity search - Function
: / o-Succinylbenzoate synthase, MenC type 2 / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel ...: / o-Succinylbenzoate synthase, MenC type 2 / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
o-succinylbenzoate synthase / o-succinylbenzoate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Malashkevich, V. / Sauder, J.M. / Ozyurt, S. / Smith, D. / Dickey, M. / Maletic, M. / Powell, A. / Gheyi, T. ...Patskovsky, Y. / Toro, R. / Malashkevich, V. / Sauder, J.M. / Ozyurt, S. / Smith, D. / Dickey, M. / Maletic, M. / Powell, A. / Gheyi, T. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.
Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. ...Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. / Swaminathan, S. / Burley, S.K. / Almo, S.C. / Glasner, M.E.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 11, 2014Group: Database references
Revision 1.4Aug 13, 2014Group: Database references
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-succinylbenzoic acid synthetase


Theoretical massNumber of molelcules
Total (without water)39,0961
Polymers39,0961
Non-polymers00
Water10,629590
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.700, 40.324, 59.223
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-succinylbenzoic acid synthetase / OSB synthetase


Mass: 39095.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: COL / Gene: menc / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q53635, UniProt: A0A0H2WWB5*PLUS, o-succinylbenzoate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 294 K / pH: 8.5
Details: O.1M TRIS-HCL, PH 8.5, 30% PEG 4000, 0.2M SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 84257 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Biso Wilson estimate: 15.69 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.032 / Net I/σ(I): 8.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WUE

1wue


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.731 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2524 3 %RANDOM
Rwork0.138 ---
obs0.139 81647 99.5 %-
all-81647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.14 Å2
2--0.14 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 0 590 3350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223055
X-RAY DIFFRACTIONr_bond_other_d0.0030.022094
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9644197
X-RAY DIFFRACTIONr_angle_other_deg1.12335158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45424.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23415560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9481519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
X-RAY DIFFRACTIONr_nbd_refined0.20.3555
X-RAY DIFFRACTIONr_nbd_other0.1630.32244
X-RAY DIFFRACTIONr_nbtor_refined0.1750.51477
X-RAY DIFFRACTIONr_nbtor_other0.0840.51536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5809
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.594
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.99522406
X-RAY DIFFRACTIONr_mcbond_other1.7982721
X-RAY DIFFRACTIONr_mcangle_it5.67432993
X-RAY DIFFRACTIONr_scbond_it7.79131435
X-RAY DIFFRACTIONr_scangle_it9.77951170
X-RAY DIFFRACTIONr_rigid_bond_restr4.4426381
X-RAY DIFFRACTIONr_sphericity_free26.885590
X-RAY DIFFRACTIONr_sphericity_bonded10.22955046
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 191 -
Rwork0.223 5912 -
obs--99.03 %

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