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- PDB-6xbv: Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) in co... -

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Basic information

Entry
Database: PDB / ID: 6xbv
TitleStreptomyces coelicolor methylmalonyl-CoA epimerase (S115T) in complex with 2-nitronate-propionyl-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
: / Chem-KFV / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 (S115T) in complex with 2-nitronate-propionyl-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)17,2286
Polymers16,0741
Non-polymers1,1545
Water4,558253
1
A: Methylmalonyl-CoA epimerase
hetero molecules

A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,45612
Polymers32,1482
Non-polymers2,30810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)69.309, 69.309, 103.562
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-323-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methylmalonyl-CoA epimerase


Mass: 16073.794 Da / Num. of mol.: 1 / Mutation: M1S, S115T
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, 258 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-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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.79 Å3/Da / Density % sol: 67.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris:HCl pH 7.0, 700 mM ammonium sulfate, and 5% PEG400
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 5, 2019 / Details: MD2 microdifractometer
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 41252 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 27.733 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Rsym value: 0.101 / Χ2: 1.012 / Net I/σ(I): 492.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 7 / Num. unique obs: 4048 / CC1/2: 0.84 / CC star: 0.956 / Rpim(I) all: 0.301 / Rrim(I) all: 1.134 / Rsym value: 0.967 / Χ2: 0.935 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.59 Å26.6 Å
Translation5.59 Å26.6 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: 1.5→26.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.888 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1791 2012 4.9 %RANDOM
Rwork0.1531 ---
obs0.1544 39173 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.01 Å2 / Biso mean: 27.733 Å2 / Biso min: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.5→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 67 275 1452
Biso mean--42.07 44.67 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171161
X-RAY DIFFRACTIONr_angle_refined_deg2.3751.7081772
X-RAY DIFFRACTIONr_angle_other_deg1.9111.6242703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4955169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92321.52872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85515208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9771511
X-RAY DIFFRACTIONr_chiral_restr0.2730.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
LS refinement shellResolution: 1.5→1.537 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.233 150 -
Rwork0.221 2835 -
obs--99.27 %

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