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Yorodumi- PDB-2i02: CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like fam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i02 | ||||||
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Title | CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION | ||||||
Components | general stress protein of COG3871 | ||||||
Keywords | OXIDOREDUCTASE / GENERAL STRESS PROTEIN OF COG3871 / PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-LIKE FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc punctiforme (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of general stress protein of COG3871 (ZP_00108720.1) from Nostoc punctiforme PCC 73102 at 1.80 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 | 2i02.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i02.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 2i02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/2i02 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i02 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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
#1: Protein | Mass: 17229.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00108720.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YS45, UniProt: B2J0D8*PLUS #2: Chemical | ChemComp-FMN / | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.38 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 277 K / pH: 4.5 Details: 0.2M NaCl, 40.0% PEG-300, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979197,0.918370 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2006 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→29.921 Å / Num. obs: 32823 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 4.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1.8→29.921 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.503 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 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. RESIDUES A1-4, A46-48, B1-4, AND B136-138 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RESIDUES B45-48 AND B61 ARE POORLY ORDERED. 5. MOLECULES FMN AND PEG-300 (P33) ARE MODELED. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 7. UNEXPLAINED DENSITY OBSERVED NEAR RESIDUES A58, A98, A101, B31-32, B61, B67.
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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 mean: 25.749 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.921 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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
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