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Yorodumi- PDB-5vrd: Crystal structure for Methylobacterium extorquens PqqCD (natural ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vrd | |||||||||
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Title | Crystal structure for Methylobacterium extorquens PqqCD (natural fusion) | |||||||||
Components | Bifunctional coenzyme PQQ synthesis protein C/D | |||||||||
Keywords | OXIDOREDUCTASE / PQQ / oxidase / alpha-helical bundle | |||||||||
Function / homology | Function and homology information pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / pyrroloquinoline quinone biosynthetic process / sulfur compound metabolic process / : / quinone binding Similarity search - Function | |||||||||
Biological species | Methylobacterium extorquens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Evans III, R.L. / Wilmot, C.M. / Esler, M.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Not published Title: Crystal structures for Methylobacterium extorquens PqqC from the CD natural fusion and the C truncation Authors: Evans III, R.L. / Esler, M.A. / Latham, J.A. / Klinman, J.P. / Wilmot, C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vrd.cif.gz | 346.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vrd.ent.gz | 280.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vrd_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 5vrd_full_validation.pdf.gz | 495.2 KB | Display | |
Data in XML | 5vrd_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 5vrd_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/5vrd ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vrd | HTTPS FTP |
-Related structure data
Related structure data | 5vrcC 1otvS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43801.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria) Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: pqqCD, MexAM1_META1p1749 / Production host: Escherichia coli (E. coli) References: UniProt: Q49150, pyrroloquinoline-quinone synthase |
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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: 2.9 Å3/Da / Density % sol: 57.52 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% ...Details: 500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% isopropanol. Water used in the well solutions contained 0.55 mM sodium azide. Hanging drops were 1 microL protein solution and 1 microL well solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→243.49 Å / Num. obs: 31557 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Net I/σ(I): 17 |
Reflection shell | Rmerge(I) obs: 0.597 / Rpim(I) all: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1otv Resolution: 2.85→243.49 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.854 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.995 / ESU R Free: 0.447 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 2.85→243.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.852→2.926 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 |
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