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- PDB-4geg: Crystal Structure of E.coli MenH Y85F Mutant -

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Basic information

Entry
Database: PDB / ID: 4geg
TitleCrystal Structure of E.coli MenH Y85F 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 / MenH Y85F mutant
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: 2.49 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)90,24126
Polymers88,4983
Non-polymers1,74323
Water7,548419
1
B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0478
Polymers29,4991
Non-polymers5477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9817
Polymers29,4991
Non-polymers4826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,21411
Polymers29,4991
Non-polymers71410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.499, 41.589, 93.081
Angle α, β, γ (deg.)90.000, 95.890, 90.000
Int Tables number5
Space group name H-MC121

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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: 29499.348 Da / Num. of mol.: 3 / Mutation: Y85F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, MenH_Y85Fmutant, 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, 442 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
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: 0.953695 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 2.489→124.587 Å / Num. all: 34120 / Num. obs: 34116 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.72 Å2 / Rmerge(I) obs: 0.324 / Rsym value: 0.324 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.489-2.627.20.95423499048400.95498
2.62-2.787.50.7842.63518247000.784100
2.78-2.987.50.5923.43289444030.592100
2.98-3.217.40.4314.63039540940.431100
3.21-3.527.30.2856.62770137740.285100
3.52-3.947.30.2088.72482734210.208100
3.94-4.557.10.15910.62168830670.159100
4.55-5.577.10.1719.41836425910.171100
5.57-7.8770.1928.11437820480.192100
7.87-124.5876.40.09711.5749211780.09799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→33.71 Å / Cor.coef. Fo:Fc: 0.9159 / Cor.coef. Fo:Fc free: 0.8429 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.431 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.27 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1723 5.05 %RANDOM
Rwork0.1767 ---
obs0.1802 34093 99.77 %-
Displacement parametersBiso max: 98.04 Å2 / Biso mean: 20.8475 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.5628 Å20 Å2-1.2953 Å2
2---2.2374 Å20 Å2
3---2.8001 Å2
Refine analyzeLuzzati coordinate error obs: 0.265 Å
Refinement stepCycle: LAST / Resolution: 2.49→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 88 419 6466
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2764SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes923HARMONIC5
X-RAY DIFFRACTIONt_it6164HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion745SEMIHARMONIC5
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_contact7428SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6164HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8370HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion3.08
LS refinement shellResolution: 2.49→2.57 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.286 159 5.6 %
Rwork0.2117 2679 -
all0.2158 2838 -
obs--99.77 %

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