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

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Basic information

Entry
Database: PDB / ID: 1fhv
TitleCRYSTAL STRUCTURE ANALYSIS OF O-SUCCINYLBENZOATE SYNTHASE FROM E. COLI COMPLEXED WITH MG AND OSB
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
2-SUCCINYLBENZOATE / o-succinylbenzoate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_seq_one_letter_code / _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: O-SUCCINYLBENZOATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9743
Polymers35,7281
Non-polymers2462
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.800, 83.000, 57.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe biological assembly is a monomer

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Components

#1: Protein O-SUCCINYLBENZOATE SYNTHASE /


Mass: 35727.703 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OSB / 2-SUCCINYLBENZOATE / O-SUCCINYLBENZOATE


Mass: 222.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 296 K / Method: microbatch
Details: 5% Peg 4000, 3% Ethylene glycol,15 mM MgCl2, 1 mM OSB, 25 mM MES, microbatch, temperature 23K
Crystal grow
*PLUS
pH: 5.4 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
25 %PEG400011
33 %ethylene glycol11
415 mM11MgCl2
51 mMOSB11
625 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7009
DetectorType: APS-1 / Detector: CCD / Date: Dec 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7009 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. all: 33959 / Num. obs: 319215 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.3
Reflection shellResolution: 1.77→1.83 Å / Rmerge(I) obs: 0.112 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 33959 / Num. measured all: 319215
Reflection shell
*PLUS
% possible obs: 99.1 % / Mean I/σ(I) obs: 12.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.77→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1675 -Random
Rwork0.185 ---
all0.185 33508 --
obs0.185 33508 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 17 335 2882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.03
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.03
X-RAY DIFFRACTIONc_plane_restr0.021

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