[English] 日本語
![](img/lk-miru.gif)
- PDB-2jio: A New Catalytic Mechanism of Periplasmic Nitrate Reductase from D... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2jio | ||||||
---|---|---|---|---|---|---|---|
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 / 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.G. / 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 |
| ||||||
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. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 983.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 990 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jimC ![]() 2jipC ![]() 2jiqC ![]() 2jirC ![]() 2v3vC ![]() 2v45C ![]() 2napS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80393.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 5 types, 815 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-MO / | ||||
#4: Chemical | #5: Chemical | ChemComp-UNX / | #6: 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 55.01 % / Description: NONE |
---|---|
Crystal grow | pH: 6 Details: 0.1M MES, PH 6.0, 6% PEG 8000 AS PURIFIED PROTEIN ONLY |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→76 Å / Num. obs: 45024 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 34.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 35 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NAP Resolution: 2.2→92.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.756 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPARISON WITH ALL THE DDNAPA STRUCTURES SHOW THAT 74 AMINO ACID RESIDUES HAVE SHOW THE HIGHEST VARIATIONS INCLUDING THE FOLLOWING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COMPARISON WITH ALL THE DDNAPA STRUCTURES SHOW THAT 74 AMINO ACID RESIDUES HAVE SHOW THE HIGHEST VARIATIONS INCLUDING THE FOLLOWING REGIONS, RESIDUES 4-7, 27- 28, 75- 76, 94-103, 183-184, 257-259, 385-392, 505-506, 533- 534, 555-556, 575-576, 617-618, 628-640, 650-658. 675-677 AND 690-694. THESE ARE ALL ON THE PROTEIN SURFACE AND INCLUDE LOOPS AND TURNS. THE AMINO ACID SIDE CHAINS WHICH SHOW MOST FLEXIBILITY INCLUDE 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. SOME OF THESE DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.15 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→92.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|