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

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Basic information

Entry
Database: PDB / ID: 2ola
TitleCrystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form
ComponentsO-succinylbenzoic acid synthetase
KeywordsLIGASE / 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: 2.45 Å
AuthorsPatskovsky, Y. / Sauder, J.M. / Ozyurt, S. / Wasserman, S.R. / Smith, D. / Dickey, M. / Maletic, M. / Reyes, C. / Gheyi, T. / Gerlt, J.A. ...Patskovsky, Y. / Sauder, J.M. / Ozyurt, S. / Wasserman, S.R. / Smith, D. / Dickey, M. / Maletic, M. / Reyes, C. / Gheyi, T. / Gerlt, J.A. / Almo, S.C. / Burley, S.K. / 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 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: 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 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.7Feb 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 1.8Aug 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
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.773, 144.773, 144.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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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: A0A0H3KH80*PLUS, o-succinylbenzoate-CoA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M Sodium malonate, PH 7.0, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 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: 2.45→50 Å / Num. all: 18662 / Num. obs: 18662 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.6 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.055 / Net I/σ(I): 7.1
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3 / Num. unique all: 1841 / Rsym value: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WUE

1wue


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.375 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26081 590 3.2 %RANDOM
Rwork0.21115 ---
all0.21276 18011 --
obs0.21276 18011 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.584 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 0 60 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9593845
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5015347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.84424.403134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.30615491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.5581513
X-RAY DIFFRACTIONr_chiral_restr0.3850.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022140
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1530.31155
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.51925
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.330
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.2642.51746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.9163.52778
X-RAY DIFFRACTIONr_scbond_it10.56841209
X-RAY DIFFRACTIONr_scangle_it13.76971063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.564 33 -
Rwork0.34 1282 -
obs-1282 100 %

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