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Yorodumi- PDB-1vrg: Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vrg | ||||||
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Title | Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA MARITIMA at 2.30 A resolution | ||||||
Components | propionyl-CoA carboxylase, beta subunit | ||||||
Keywords | LIGASE / TM0716 / propionyl-CoA carboxylase / beta subunit / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of propionyl-CoA carboxylase, beta subunit (TM0716) from THERMOTOGA MARITIMA at 2.30 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vrg.cif.gz | 612 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vrg.ent.gz | 504.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vrg ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vrg | HTTPS FTP |
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-Related structure data
Related structure data | 1on3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 515 / Label seq-ID: 13 - 527
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-Components
#1: Protein | Mass: 58602.832 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0716 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZH5, acetyl-CoA carboxylase #2: Chemical | #3: Chemical | ChemComp-BCT / #4: Water | ChemComp-HOH / | |
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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: 2.46 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6 Details: 0.2M Li2SO4, 35.0% MPD, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96112 |
Detector | Type: APS / Detector: CCD / Date: Aug 8, 2003 Details: double crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96112 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.36 Å / Num. obs: 148537 / % possible obs: 96.76 % / Redundancy: 7.19 % / Biso Wilson estimate: 41.19 Å2 / Rsym value: 0.124 / Net I/σ(I): 11.58 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.82 % / Mean I/σ(I) obs: 1.32 / Num. unique all: 12848 / Rsym value: 0.553 / % possible all: 84.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ON3 Resolution: 2.3→45.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.119 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. METAL SITE WAS MODELED AS MG. ANOMALOUS DIFFERENCE FOURIERS DID NOT SHOW A PEAK AT MG LOCATIONS.
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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 mean: 29.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.36 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7541 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.361 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 515 / Label seq-ID: 13 - 527
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