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- PDB-1jc5: Crystal Structure of Native Methylmalonyl-CoA Epimerase -

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Basic information

Entry
Database: PDB / ID: 1jc5
TitleCrystal Structure of Native Methylmalonyl-CoA Epimerase
ComponentsMethylmalonyl-CoA Epimerase
KeywordsISOMERASE / epimerisation / methylmalonyl-CoA / vicinal oxygen chelate superfamily / metal-assisted catalysis
Function / homology
Function and homology information


methylmalonyl-CoA epimerase / methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / metal ion binding
Similarity search - Function
: / Methylmalonyl-CoA epimerase / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Methylmalonyl-CoA epimerase
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMc Carthy, A.A. / Baker, H.M. / Shewry, S.C. / Patchett, M.L. / Baker, E.N.
Citation
Journal: Structure / Year: 2001
Title: Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.
Authors: McCarthy, A.A. / Baker, H.M. / Shewry, S.C. / Patchett, M.L. / Baker, E.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression, Crystallization and Preliminary Characterization of Methylmalonyl Coenzyme A Epimerase from Propionibacterium shermanii
Authors: Mc Carthy, A.A. / Baker, H.M. / Shewry, S.C. / Kagawa, T.F. / Saafi, E. / Patchett, M.L. / Baker, E.N.
History
DepositionJun 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Methylmalonyl-CoA Epimerase
B: Methylmalonyl-CoA Epimerase
C: Methylmalonyl-CoA Epimerase
D: Methylmalonyl-CoA Epimerase
E: Methylmalonyl-CoA Epimerase
F: Methylmalonyl-CoA Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39416
Polymers100,4336
Non-polymers96110
Water2,306128
1
A: Methylmalonyl-CoA Epimerase
B: Methylmalonyl-CoA Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8626
Polymers33,4782
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-99 kcal/mol
Surface area13860 Å2
MethodPISA
2
C: Methylmalonyl-CoA Epimerase
D: Methylmalonyl-CoA Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7665
Polymers33,4782
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-87 kcal/mol
Surface area13610 Å2
MethodPISA
3
E: Methylmalonyl-CoA Epimerase
F: Methylmalonyl-CoA Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7665
Polymers33,4782
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-87 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.985, 114.020, 156.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer

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Components

#1: Protein
Methylmalonyl-CoA Epimerase


Mass: 16738.908 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Plasmid: pTEEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VQN0, methylmalonyl-CoA epimerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: PEG 2000 (MME), sodium acetate, ammonium sulfate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mammonium sulfate1reservoir
20.1 Msodium acetate1reservoir
3PEG2000MME1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1998 / Details: synchrotron
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→14.98 Å / Num. all: 50685 / Num. obs: 50033 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 13.1 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 70 / Limit l min: 0 / Observed criterion F max: 369750.46 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.043 / Net I/σ(I): 31.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.143 / % possible all: 99
Reflection
*PLUS
% possible obs: 97.8 % / Num. measured all: 201176
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 85.8 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→14.98 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 5042 10.1 %Random
Rwork0.248 ---
all-50033 --
obs-50033 97.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 27.1422 Å2 / ksol: 0.342291 e/Å3
Displacement parametersBiso max: 64.92 Å2 / Biso mean: 25.55 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1-6.69 Å20 Å20 Å2
2---5 Å20 Å2
3----1.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 50 128 7090
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.73
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.340.32781610.50.26869290.0116346572491.1
2.3-2.420.2695969.30.2755520.0116376614896.4
2.42-2.570.27765010.20.27855350.0116370618597.1
2.57-2.770.2736089.50.27556230.0116379623197.7
2.77-3.050.2815979.40.28256740.0126381627198.3
3.05-3.480.28267010.40.27857250.0116460639599
3.48-4.370.226649100.22257940.0096486644399.3
4.37-14.980.195669100.19959670.0086720663698.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramse_protein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.268

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