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- PDB-2v45: A New Catalytic Mechanism of Periplasmic Nitrate Reductase from D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v45 | ||||||
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Title | A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand | ||||||
![]() | PERIPLASMIC NITRATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / NITRATE ASSIMILATION / NITROGENOUS ACCEPTOR / IRON / TRANSPORT / MOLYBDENUM / PERIPLASMIC / DISULFIDE BOND / ELECTRON TRANSPORT / IRON-SULFUR / METAL-BINDING / DISSIMILATORY NITRATE REDUCTASE / MOLYBDOPTERIN COFACTOR / SULFIDO LIGAND / 4FE-4S CLUSTER / ELECTRON PARAMAGNETIC RESONANCE | ||||||
Function / homology | ![]() nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / molybdopterin cofactor binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Najmudin, S. / Gonzalez, P.J. / Trincao, J. / Coelho, C. / Mukhopadhyay, A. / Romao, C.C. / Moura, I. / Moura, J.J. / Brondino, C.D. / Romao, M.J. | ||||||
![]() | ![]() Title: Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum. Authors: Najmudin, S. / Gonzalez, P.J. / Trincao, J. / Coelho, C. / Mukhopadhyay, A. / Cerqueira, N.M.F.S.A. / Romao, C.C. / Moura, I. / Moura, J.J.G. / Brondino, C.D. / Romao, M.J. #1: Journal: J.Biol.Inorg.Chem. / Year: 2006 Title: Epr and Redox Properties of Periplasmic Nitrate Reductase from Desulfovibrio Desulfuricans Atcc 27774 Authors: Gonzalez, P.J. / Rivas, M.G. / Brondino, C.D. / Bursakov, S.A. / Moura, I. / Moura, J.J.G. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.5 KB | Display | ![]() |
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PDB format | ![]() | 132.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 903.1 KB | Display | ![]() |
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Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jimC ![]() 2jioC ![]() 2jipC ![]() 2jiqC ![]() 2jirC ![]() 2v3vC ![]() 2napS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 80392.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 526 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/LCP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/LCP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||||
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#3: Chemical | ChemComp-MO / | ||||||
#4: Chemical | #5: Chemical | ChemComp-UNX / | #6: Chemical | ChemComp-LCP / | #7: Water | ChemComp-HOH / | |
-Details
Compound details | ESSENTIAL FUNCTION FOR NITRATE ASSIMILATINonpolymer details | THE RESIDUE A 813 WAS ORIGINALLY DEPOSITED AS A ISOLATED SULFUR ATOM. AS PART OF REMEDIATION, THIS ...THE RESIDUE A 813 WAS ORIGINALLY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.34 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: COCRYSTALLISATION WITH 20MM OF KCLO4 (PERCHLORATE) IN 200MM OF DDNAPA (IE PROTEIN) WHICH HAD BEEN REDUCED BY DITHIONITE IN ANAEROBIC CONDITIONS AND THEN AIR REOXIDISED. THE SAMPLE WAS LEFT ...Details: COCRYSTALLISATION WITH 20MM OF KCLO4 (PERCHLORATE) IN 200MM OF DDNAPA (IE PROTEIN) WHICH HAD BEEN REDUCED BY DITHIONITE IN ANAEROBIC CONDITIONS AND THEN AIR REOXIDISED. THE SAMPLE WAS LEFT AT ROOM TEMPERATURE FOR SEVERAL MONTHS BEFORE SETTING UP CRYSTALLISATIONS IN 0.1M MES, PH 6.5, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04453 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→65.09 Å / Num. obs: 33558 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NAP Resolution: 2.4→91.67 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.234 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICA E.G. THE AMINO ACID SIDE CHAINS WHICH SHOW MOST FLEXIBILITY INCLUDING THE FOLLOWING LYSINES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICA E.G. THE AMINO ACID SIDE CHAINS WHICH SHOW MOST FLEXIBILITY INCLUDING THE FOLLOWING LYSINES (7, 27, 75, 259, 380, 636, 722), ARGININES (4, 544, 652), GLUTAMATES (6, 257, 287, 386, 541, 608, 647, 648) AND GLUTAMINES (193, 510). SOME OF THESE HAVE BEEN ASSIGNED WITH ALTERNATE CONFORMATIONS.
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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: 54.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→91.67 Å
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Refine LS restraints |
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