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- PDB-4gec: Crystal Structure of E.coli MenH R124A Mutant -

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Basic information

Entry
Database: PDB / ID: 4gec
TitleCrystal Structure of E.coli MenH R124A Mutant
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 / mutant R124A / MenH mutant R124A
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: 2.5 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
DepositionAug 1, 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 1.3Feb 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)88,93212
Polymers88,2883
Non-polymers6459
Water4,179232
1
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8116
Polymers29,4291
Non-polymers3825
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)29,5613
Polymers29,4291
Non-polymers1322
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)29,5613
Polymers29,4291
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.144, 115.144, 469.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 29429.234 Da / Num. of mol.: 3 / Mutation: R124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, MenH_R124Amutant, 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

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Non-polymers , 5 types, 241 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 4.41 Å3/Da / Density % sol: 72.1 %
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: MX1 / Wavelength: 0.953692 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 2.5→117.444 Å / Num. all: 54795 / Num. obs: 54795 / % possible obs: 99.4 % / Redundancy: 14.9 % / Biso Wilson estimate: 61.48 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.6415.21.8471.811862478161.84799
2.64-2.815.22.611281174331.26799.1
2.8-2.9915.14.410578769970.75899.2
2.99-3.2315.17.69948865960.43199.3
3.23-3.541514.49085560540.2299.5
3.54-3.9514.923.88238155260.12699.6
3.95-4.5614.836.67258549050.07699.7
4.56-5.5914.7386152341980.07199.8
5.59-7.9114.341.74744933200.06199.9
7.91-81.41913.20.02777.82564619500.02799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→81.42 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.187 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 2792 5.1 %RANDOM
Rwork0.1936 ---
obs0.1951 54795 99.13 %-
Displacement parametersBiso max: 141.12 Å2 / Biso mean: 49.133 Å2 / Biso min: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.7133 Å20 Å20 Å2
2---3.7133 Å20 Å2
3---7.4265 Å2
Refine analyzeLuzzati coordinate error obs: 0.322 Å
Refinement stepCycle: LAST / Resolution: 2.5→81.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5923 0 33 232 6188
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2735SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes917HARMONIC5
X-RAY DIFFRACTIONt_it6087HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion742SEMIHARMONIC5
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_contact7679SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6087HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8267HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion3.06
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 215 5.43 %
Rwork0.2433 3743 -
all0.2448 3958 -
obs--99.13 %

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