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- PDB-6wf6: Streptomyces coelicolor methylmalonyl-CoA epimerase -

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Basic information

Entry
Database: PDB / ID: 6wf6
TitleStreptomyces coelicolor methylmalonyl-CoA epimerase
ComponentsMethylmalonyl-CoA epimerase
KeywordsISOMERASE / Epimerase / acid-base / enol / enolate
Function / homology
Function and homology information


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
: / DI(HYDROXYETHYL)ETHER / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 / Derived calculations / Category: citation / database_2 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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
B: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4506
Polymers32,1202
Non-polymers3304
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-46 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.224, 75.849, 80.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methylmalonyl-CoA epimerase / Ethylmalonyl-CoA epimerase


Mass: 16059.767 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 300 mM sodium chloride, 100 mM bis-tris:HCl pH 7.0, 26% PEG 3350, 5% PEG 400
Temp details: room temperature

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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-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 19, 2017 / Details: MD2 microdifractometer
Diffraction measurementDetails: 1.00 degrees, 5.02 sec, detector distance 140.00 mm
Method: \w scans
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionAv R equivalents: 0.165 / Number: 411126
ReflectionResolution: 1.39→30 Å / Num. obs: 58310 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.067 / Rrim(I) all: 0.178 / Rsym value: 0.165 / Χ2: 1.043 / Net I/av σ(I): 11.774 / Net I/σ(I): 6.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7 % / Rmerge(I) obs: 1.443 / Mean I/σ(I) obs: 2 / Num. unique obs: 5716 / Rsym value: 1.443 / % possible all: 100
Cell measurementReflection used: 411126

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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: 1.39→29.59 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.2028 / WRfactor Rwork: 0.1754 / FOM work R set: 0.8602 / SU B: 1.116 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0548 / SU Rfree: 0.0574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 2938 5 %RANDOM
Rwork0.155 ---
obs0.1564 55302 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: 71.56 Å2 / Biso mean: 18.085 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0 Å2
2---0.99 Å20 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.39→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 16 391 2574
Biso mean--33.52 31.41 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132412
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172221
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.6413294
X-RAY DIFFRACTIONr_angle_other_deg1.5041.5825160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3245329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59121.701147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21615411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7921522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 1.395→1.431 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 201 -
Rwork0.255 3905 -
all-4106 -
obs--96.34 %

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