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- PDB-6wfi: Methylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6wfi
TitleMethylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA
ComponentsMethylmalonyl-CoA epimerase
KeywordsISOMERASE / Epimerase / acid-base / enol / enolate
Function / homology
Function and homology information


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
: / Chem-KFV / DI(HYDROXYETHYL)ETHER / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsStunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R.
CitationJournal: Chembiochem / Year: 2022
Title: Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase.
Authors: Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Source and taxonomy / Category: citation / database_2 / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3207
Polymers16,0601
Non-polymers1,2606
Water5,116284
1
A: Methylmalonyl-CoA epimerase
hetero molecules

A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,64014
Polymers32,1202
Non-polymers2,52012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)68.837, 68.837, 103.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methylmalonyl-CoA epimerase


Mass: 16059.767 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO5398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L2C2

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Non-polymers , 6 types, 290 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-KFV / [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium


Mass: 867.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N8O19P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 34.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.6 M ammonium sulfate, 5% PEG 400

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 8, 2017 / Details: MD2 Micro Diffractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. obs: 52867 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.016 / Rrim(I) all: 0.061 / Rsym value: 0.059 / Χ2: 1.051 / Net I/av σ(I): 38.672 / Net I/σ(I): 14.2 / Num. measured all: 752533
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 6.516 / Num. unique obs: 5196 / Rsym value: 0.47 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.44 Å25.84 Å
Translation5.44 Å25.84 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.7.17phasing
SCALEPACKdata scaling
ARP/wARPmodel building
Cootmodel building
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JC5

1jc5


Resolution: 1.37→25.86 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.56 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 2548 4.8 %RANDOM
Rwork0.1474 ---
obs0.1486 50250 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.83 Å2 / Biso mean: 19.115 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.37→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 74 314 1497
Biso mean--31.95 35.84 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131323
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171195
X-RAY DIFFRACTIONr_angle_refined_deg2.6171.7041825
X-RAY DIFFRACTIONr_angle_other_deg1.6531.6212793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4525177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57421.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54515218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8271511
X-RAY DIFFRACTIONr_chiral_restr0.2870.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021512
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02286
LS refinement shellResolution: 1.37→1.405 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 181 -
Rwork0.22 3630 -
all-3811 -
obs--98.68 %

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