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Yorodumi- PDB-3fkh: Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fkh | ||||||
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Title | Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution | ||||||
Components | Putative pyridoxamine 5'-phosphate oxidase | ||||||
Keywords | OXIDOREDUCTASE / NP_601736.1 / Putative pyridoxamine 5'-phosphate oxidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function | ||||||
Function / homology | Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Roll / Mainly Beta / : Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 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 | 3fkh.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkh.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fkh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3fkh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3fkh_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 3fkh_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkh ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 15986.668 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Gene: cg2794, NP_601736.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M2U2 #2: Chemical | ChemComp-P33 / #3: Chemical | ChemComp-CA / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.37 Å3/Da / Density % sol: 48.17 % Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97962 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2008 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.51→29.54 Å / Num. obs: 31540 / % possible obs: 96 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.655 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.51→29.54 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.797 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.681 / ESU R Free: 0.335 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. PEG-8000 FRAGMENTS (P33) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.48 Å2 / Biso mean: 52.455 Å2 / Biso min: 14.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→29.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.507→2.572 Å / Total num. of bins used: 20
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