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Yorodumi- PDB-2vmj: Type 1 Copper-Binding Loop of Nitrite Reductase mutant: 130- CAPE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vmj | ||||||
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Title | Type 1 Copper-Binding Loop of Nitrite Reductase mutant: 130- CAPEGMVPWHVVSGM-144 to 130-CTPHPFM-136 | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / CUPREDOXIN / TYPE 1 COPPER / TYPE 2 COPPER / ELECTRON TRANSFER / LOOP-DIRECTED MUTAGENESIS / COPPER-CONTAINING NITRITE REDUCTASE | ||||||
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 XYLOSOXYDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sato, K. / Firbank, S.J. / Li, C. / Banfield, M.J. / Dennison, C. | ||||||
Citation | Journal: Chemistry / Year: 2008 Title: The Importance of the Long Type 1 Copper-Binding Loop of Nitrite Reductase for Structure and Function. Authors: Sato, K. / Firbank, S.J. / Li, C. / Banfield, M.J. / Dennison, C. | ||||||
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 | 2vmj.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vmj.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vmj_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 2vmj_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 2vmj_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2vmj_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vmj ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vmj | HTTPS FTP |
-Related structure data
Related structure data | 2vn3C 1oe1S 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: 35933.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-154,168-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS (bacteria) Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O68601 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | Sequence details | THE STRUCTURE BELOW DESCRIBES A MUTANT, WHERE 130-CAPEGMVPWH | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 50 MM HEPES PH 7.0, 5 MM ZNCL2 AND 10 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.33 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.33 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.5 Å / Num. obs: 14625 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 2.5→37.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.274 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.256 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→37.53 Å
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