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Yorodumi- PDB-6xbv: Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xbv | ||||||
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Title | Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) in complex with 2-nitronate-propionyl-CoA | ||||||
Components | Methylmalonyl-CoA epimerase | ||||||
Keywords | ISOMERASE/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 / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Stunkard, L.M. / Boram, T.J. / Benjamin, A.B. / Bower, J.B. / Lohman, J.R. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xbv.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xbv.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xbv_validation.pdf.gz | 691 KB | Display | wwPDB validaton report |
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Full document | 6xbv_full_validation.pdf.gz | 693.4 KB | Display | |
Data in XML | 6xbv_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 6xbv_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xbv ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xbv | HTTPS FTP |
-Related structure data
Related structure data | 1jc5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-KFV / [ | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.53 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2019 / Details: MD2 microdifractometer |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.01 Å2 / Biso mean: 27.733 Å2 / Biso min: 15.72 Å2
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Refinement step | Cycle: final / Resolution: 1.5→26.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.537 Å / Rfactor Rfree error: 0
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