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- PDB-1fhu: CRYSTAL STRUCTURE ANALYSIS OF O-SUCCINYLBENZOATE SYNTHASE FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1fhu
TitleCRYSTAL STRUCTURE ANALYSIS OF O-SUCCINYLBENZOATE SYNTHASE FROM E. COLI
ComponentsO-SUCCINYLBENZOATE SYNTHASE
KeywordsOXIDOREDUCTASE / Enolase superfamily
Function / homology
Function and homology information


o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / hydro-lyase activity / magnesium ion binding
Similarity search - Function
: / MenC, N-terminal domain / o-Succinylbenzoate synthase, MenC type1 / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal ...: / MenC, N-terminal domain / o-Succinylbenzoate synthase, MenC type1 / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsRayment, I. / Thompson, T.B. / Gerlt, J.A.
CitationJournal: Biochemistry / Year: 2000
Title: Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate.
Authors: Thompson, T.B. / Garrett, J.B. / Taylor, E.A. / Meganathan, R. / Gerlt, J.A. / Rayment, I.
History
DepositionAug 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-SUCCINYLBENZOATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)35,5131
Polymers35,5131
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.1, 70.0, 80.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer

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Components

#1: Protein O-SUCCINYLBENZOATE SYNTHASE /


Mass: 35512.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: MODIFIED PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P29208
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 6.75
Details: 27% ME-PEG 5000, 267 mM NaCl, 50 mM Mes, 15-20 mg/ml protein, pH 6.75, micro batch, temperature 23K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein11
227 %mPEG500011
3267 mM11NaCl
450 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537
DetectorType: SBC / Detector: CCD / Date: Dec 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 36924 / Num. obs: 420933 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 11 % / Rmerge(I) obs: 0.294 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 36924
Reflection shell
*PLUS
Mean I/σ(I) obs: 11

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Processing

Software
NameClassification
SOLVEphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.65→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1846 -Random
Rwork0.195 ---
all0.195 36924 --
obs0.195 36924 99 %-
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 0 351 2632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.03
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.11
X-RAY DIFFRACTIONt_plane_restr0.021

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