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- PDB-6wf7: Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+ -

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Basic information

Entry
Database: PDB / ID: 6wf7
TitleMethylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+
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
(S)-Methylmalonyl-Coenzyme A / METHYLMALONYL-COENZYME A / AMMONIUM ION / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)18,0056
Polymers16,0601
Non-polymers1,9455
Water3,639202
1
A: Methylmalonyl-CoA epimerase
hetero molecules

A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01012
Polymers32,1202
Non-polymers3,89110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6130 Å2
ΔGint-115 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.537, 68.537, 103.150
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-203-

SO4

21A-332-

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 , 5 types, 207 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MC0 / (S)-Methylmalonyl-Coenzyme A / (3S,5R,9R,20S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8,20-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicosan-21-oic acid 3,5-dioxide (non-preferred name)


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MCA / METHYLMALONYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.3 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: Jul 16, 2017 / Details: MD2 Micro Diffractometer
Diffraction measurementDetails: 1.00 degrees, 3.06 sec, detector distance 200.00 mm
Method: \w scans
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionAv R equivalents: 0.087 / Number: 521570
ReflectionResolution: 1.55→30 Å / Num. obs: 36333 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Rsym value: 0.087 / Χ2: 1.015 / Net I/av σ(I): 27 / Net I/σ(I): 11.4 / Num. measured all: 521570
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3564 / Rsym value: 0.614 / % possible all: 100
Cell measurementReflection used: 521570

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
ARP/wARPmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JC5

1jc5


Resolution: 1.55→29.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1951 / WRfactor Rwork: 0.1803 / FOM work R set: 0.9022 / SU B: 0.84 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0539 / SU Rfree: 0.0552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 1719 4.7 %RANDOM
Rwork0.1513 ---
obs0.1522 34548 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 799 Å2 / Biso mean: 24.875 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.55→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 73 217 1399
Biso mean--54.2 40.2 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131282
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171143
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.6511764
X-RAY DIFFRACTIONr_angle_other_deg1.5881.5792662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58921.62274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0521510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
LS refinement shellResolution: 1.55→1.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 130 -
Rwork0.215 2433 -
all-2563 -
obs--96.94 %

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