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- PDB-4gdm: Crystal Structure of E.coli MenH -

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Basic information

Entry
Database: PDB / ID: 4gdm
TitleCrystal Structure of E.coli MenH
Components2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
KeywordsLYASE / menaquinone biosynthesis / alpha beta hydrolase / 2-succinyl-6-hydroxy-2 / 4-cyclohexadiene-1-carboxylate synthase / MenH
Function / homology
Function and homology information


2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity / menaquinone biosynthetic process / cytosol
Similarity search - Function
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsJohnston, J.M. / Baker, E.N. / Guo, Z. / Jiang, M.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structures of E. coli Native MenH and Two Active Site Mutants.
Authors: Johnston, J.M. / Jiang, M. / Guo, Z. / Baker, E.N.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Feb 4, 2015Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,12911
Polymers88,5463
Non-polymers5838
Water1,17165
1
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6473
Polymers29,5151
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8355
Polymers29,5151
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6473
Polymers29,5151
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.664, 116.664, 476.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / SHCHC synthase


Mass: 29515.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, yfbB / Plasmid: pETM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P37355, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium Citrate, Ammonium sulfate, Lithium sulfate, pH 5.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→45.774 Å / Num. all: 43461 / Num. obs: 43437 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 17.5 % / Biso Wilson estimate: 69.92 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 22.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4266

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→45.77 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9149 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.228 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2182 5.02 %RANDOM
Rwork0.1919 ---
obs0.1935 43432 99.94 %-
Displacement parametersBiso max: 135.83 Å2 / Biso mean: 53.7247 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--2.0462 Å20 Å20 Å2
2---2.0462 Å20 Å2
3---4.0924 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.75→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 29 65 6043
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2753SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes921HARMONIC5
X-RAY DIFFRACTIONt_it6110HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion743SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6877SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6110HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8297HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3022 153 4.92 %
Rwork0.2726 2954 -
all0.2742 3107 -
obs--99.94 %

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