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Yorodumi- PDB-2nap: DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nap | |||||||||
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Title | DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS | |||||||||
Components | PROTEIN (PERIPLASMIC NITRATE REDUCTASE) | |||||||||
Keywords | OXIDOREDUCTASE / NITROGENOUS ACCEPTOR / DISSIMILATORY NITRATE REDUCTASE / MULTIWAVELENGTH ANOMALOUS DIFFRACTION / MOLYBDOPTERIN COFACTOR / [4FE-4S] CLUSTER | |||||||||
Function / homology | Function and homology information nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | |||||||||
Authors | Dias, J.M. / Than, M. / Humm, A. / Huber, R. / Bourenkov, G. / Bartunik, H. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. ...Dias, J.M. / Than, M. / Humm, A. / Huber, R. / Bourenkov, G. / Bartunik, H. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. / Moura, J. / Moura, I. / Romao, M.J. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods. Authors: Dias, J.M. / Than, M.E. / Humm, A. / Huber, R. / Bourenkov, G.P. / Bartunik, H.D. / Bursakov, S. / Calvete, J. / Caldeira, J. / Carneiro, C. / Moura, J.J. / Moura, I. / Romao, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nap.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nap.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/2nap ftp://data.pdbj.org/pub/pdb/validation_reports/na/2nap | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80392.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Cellular location: PERIPLASM / References: GenBank: CAA77019, UniProt: P81186*PLUS |
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-Non-polymers , 5 types, 600 molecules
#2: Chemical | ChemComp-SF4 / | ||||
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#3: Chemical | ChemComp-MO / | ||||
#4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 59 % |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
Crystal | *PLUS Density % sol: 55 % |
Crystal grow | *PLUS Method: vapor diffusion |
Components of the solutions | *PLUS Common name: PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.7219,1.7389,1.1000 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→25 Å / Num. obs: 69767 / % possible obs: 98 % / Redundancy: 3.4 % / Rsym value: 0.053 / Net I/σ(I): 25.9 | ||||||||||||
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.436 / % possible all: 93.5 | ||||||||||||
Reflection | *PLUS Num. measured all: 1048219 / Rmerge(I) obs: 0.053 | ||||||||||||
Reflection shell | *PLUS % possible obs: 93.5 % / Rmerge(I) obs: 0.436 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.01 |