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Yorodumi- PDB-1wae: Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wae | ||||||
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Title | Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nitrite Reductase | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / COPPER PROTEIN | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ALCALIGENES XYLOSOXYDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ellis, M.J. / Antonyuk, S.V. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2004 Title: Observation of an Unprecedented Cu Bis-His Site: Crystal Structure of the H129V Mutant of Nitrite Reductase Authors: Ellis, M.J. / Antonyuk, S.V. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wae.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wae.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wae_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 1wae_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 1wae_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1wae_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/1wae ftp://data.pdbj.org/pub/pdb/validation_reports/wa/1wae | HTTPS FTP |
-Related structure data
Related structure data | 1ndtS 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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Unit cell |
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-Components
#1: Protein | Mass: 36531.512 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALCALIGENES XYLOSOXYDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NCIMB 11015 / Variant (production host): DE3 References: UniProt: O68601, EC: 1.7.99.3, nitrite reductase (NO-forming) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: 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: 3.2 Å3/Da / Density % sol: 63 % |
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Crystal grow | pH: 6.5 Details: 100MM MES BUFFER PH 6.5 200MM ZNSO4, 40-50% PEG550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 35547 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NDT Resolution: 1.95→30.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.84 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.133 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30.01 Å
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Refine LS restraints |
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