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- PDB-1jc4: Crystal Structure of Se-Met Methylmalonyl-CoA Epimerase -

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Basic information

Entry
Database: PDB / ID: 1jc4
TitleCrystal Structure of Se-Met Methylmalonyl-CoA Epimerase
ComponentsMethylmalonyl-CoA epimerase
KeywordsISOMERASE / vicinal oxygen chelate superfamily / methylmalonyl-CoA
Function / homology
Function and homology information


methylmalonyl-CoA epimerase / methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process
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 / MAD / Resolution: 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 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84510
Polymers68,2694
Non-polymers5766
Water1,62190
1
A: Methylmalonyl-CoA epimerase
B: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4235
Polymers34,1342
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-84 kcal/mol
Surface area13820 Å2
MethodPISA
2
C: Methylmalonyl-CoA epimerase
D: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4235
Polymers34,1342
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-85 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.600, 78.620, 89.430
Angle α, β, γ (deg.)90.00, 91.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer

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Components

#1: Protein
Methylmalonyl-CoA epimerase


Mass: 17067.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Plasmid: pProEXHTa / 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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 2000 (MME), sodium acetate, ammonium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / PH range low: 4.3 / PH range high: 4.2
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: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.99→19.85 Å / Num. all: 41059 / Num. obs: 39229 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 13.5 Å2 / Limit h max: 21 / Limit h min: -21 / Limit k max: 39 / Limit k min: -21 / Limit l max: 44 / Limit l min: 0 / Observed criterion F max: 431328.6 / Observed criterion F min: 0.45 / Rmerge(I) obs: 0.062 / Net I/σ(I): 25
Reflection shellResolution: 2→2.13 Å / Redundancy: 5 % / Rmerge(I) obs: 0.802 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 204757
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.354

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.85 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3930 10 %random
Rwork0.228 ---
all-39229 --
obs-39229 96.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 31.3284 Å2 / ksol: 0.335152 e/Å3
Displacement parametersBiso max: 62.28 Å2 / Biso mean: 29.41 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å2-6.04 Å2
2---3.96 Å20 Å2
3----1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 30 90 4716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg23.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.68
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 (%)
2-2.130.30764410.50.26455000.0125132460490.5
2.09-2.20.2544779.40.25342510.0125074472893.2
2.2-2.340.2324899.70.23243050.015056479494.8
2.34-2.520.24346290.24444290.0115108489195.8
2.52-2.770.2574919.60.25844580.0125096494997.1
2.77-3.170.2595029.80.2644910.0125101499397.9
3.17-3.990.22152210.20.2245800.015122510299.6
3.99-19.850.1865159.90.18746530.0085194516899.5
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 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.2
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: 0.307 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.264

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