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Yorodumi- PDB-2x1k: H71S mutant of the antibiotic resistance protein NimA from Deinoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x1k | ||||||
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Title | H71S mutant of the antibiotic resistance protein NimA from Deinococcus radiodurans | ||||||
Components | NIMA-RELATED PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / ACETATE ION / NimA-related protein Function and homology information | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Leiros, H.S. / Brandsdal, B.O. / McSweeney, S.M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2010 Title: Biophysical Characterization and Mutational Analysis of the Antibiotic Resistance Protein Nima from Deinococcus Radiodurans. Authors: Leiros, H.S. / Brandsdal, B.O. / Mcsweeney, S.M. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Structural Basis of 5-Nitroimidazole Antibiotic Resistance: The Crystal Structure of Nima from Deinococcus Radiodurans. Authors: Leiros, H.-K.S. / Kozielski-Stuhrmann, S. / Kapp, U. / Terradot, L. / Leonard, G.A. / Mcsweeney, S.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x1k.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x1k.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 2x1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x1k_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 2x1k_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 2x1k_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2x1k_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/2x1k ftp://data.pdbj.org/pub/pdb/validation_reports/x1/2x1k | HTTPS FTP |
-Related structure data
Related structure data | 2x1jC 1w3oS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 24398.127 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR(DE3)PLYSS / References: UniProt: Q9RW27 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6 Details: 13MG/ML PROTEIN, 0.6M SODIUM ACETATE, 0.1M BUFFER PH 6 (CITRATE/MES). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 29814 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 0 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 0 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W3O Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.615 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.861 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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