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Yorodumi- PDB-2bwd: Atomic Resolution Structure of Achromobacter cycloclastes Cu Nitr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bwd | ||||||
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Title | Atomic Resolution Structure of Achromobacter cycloclastes Cu Nitrite Reductase with Endogenously bound Nitrite and NO | ||||||
Components | COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DENITRIFICATION / CATALYSIS / ENZYME MECHANISM / NITRATE ASSIMILATION | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ACHROMOBACTER CYCLOCLASTES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Antonyuk, S.V. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Atomic Resolution Structures of Resting-State, Substrate- and Product-Complexed Cu-Nitrite Reductase Provide Insight Into Catalytic Mechanism Authors: 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 | 2bwd.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bwd.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/2bwd ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bwd | HTTPS FTP |
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-Related structure data
Related structure data | 2bw4SC 2bw5C 2bwiC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37059.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACHROMOBACTER CYCLOCLASTES (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming) |
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-Non-polymers , 6 types, 572 molecules
#2: Chemical | #3: Chemical | ChemComp-MLI / | #4: Chemical | #5: Chemical | ChemComp-HOA / | #6: Chemical | ChemComp-NO2 / | #7: 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 Å3/Da / Density % sol: 36.6 % |
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Crystal grow | pH: 4.75 Details: 1.6 M AMMONIUM SULPHATE, 100MM SODIUM ACETATE, PH 4.75 |
-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: Apr 8, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→30 Å / Num. obs: 103981 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BW4 Resolution: 1.15→30 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.977 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / 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: 9.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→30 Å
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Refine LS restraints |
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