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- PDB-6xbq: Streptomyces coelicolor methylmalonyl-CoA epimerase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6xbq
TitleStreptomyces coelicolor methylmalonyl-CoA epimerase in complex with carboxy-carba(dethia)-CoA
ComponentsMethylmalonyl-CoA epimerase
KeywordsISOMERASE/INHIBITOR / Methylmalonyl-CoA / epimerase / enol/enolate / enol/enolate analog / ISOMERASE / ISOMERASE-INHIBITOR complex
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
CARBOXYMETHYLDETHIA COENZYME *A / : / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsStunkard, L.M. / Boram, T.J. / Benjamin, A.B. / Bower, J.B. / Lohman, J.R.
CitationJournal: To Be Published
Title: Streptomyces coelicolor methylmalonyl-CoA epimerase in complex with carboxy-carba(dethia)-CoA
Authors: Stunkard, L.M. / Boram, T.J. / Benjamin, A.B. / Bower, J.B. / Lohman, J.R.
History
DepositionJun 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,1045
Polymers16,0601
Non-polymers1,0454
Water3,387188
1
A: Methylmalonyl-CoA epimerase
hetero molecules

A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,20910
Polymers32,1202
Non-polymers2,0898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6300 Å2
ΔGint-92 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.504, 68.504, 103.315
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-317-

HOH

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Components

#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 (strain ATCC BAA-471 / A3(2) / M145) (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.: 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-CMX / CARBOXYMETHYLDETHIA COENZYME *A


Mass: 793.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 66.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2 M ammonium sulfate, 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-F / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 25, 2018 / Details: MD2 microdiffractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 30657 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.041 / Rrim(I) all: 0.153 / Rsym value: 0.139 / Χ2: 1.017 / Net I/σ(I): 270.4
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 2999 / CC1/2: 0.874 / CC star: 0.966 / Rpim(I) all: 0.243 / Rrim(I) all: 0.919 / Rsym value: 0.872 / Χ2: 1.042 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.56 Å28.55 Å
Translation5.56 Å28.55 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
ARP/wARPmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JC5

1jc5


Resolution: 1.64→28.56 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.168 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0632 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1752 1545 5.1 %RANDOM
Rwork0.1544 ---
obs0.1555 29049 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.59 Å2 / Biso mean: 28.474 Å2 / Biso min: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.64→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 62 199 1370
Biso mean--45.02 43.41 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131228
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171101
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.7011682
X-RAY DIFFRACTIONr_angle_other_deg1.6221.6222552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4055154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2721.61868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38815193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5441510
X-RAY DIFFRACTIONr_chiral_restr0.3040.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
LS refinement shellResolution: 1.643→1.685 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 104 -
Rwork0.215 2018 -
all-2122 -
obs--95.97 %

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