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- PDB-1ogy: Crystal structure of the heterodimeric nitrate reductase from Rho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ogy | ||||||
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Title | Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides | ||||||
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![]() | OXIDOREDUCTASE / NITRATE REDUCTASE | ||||||
Function / homology | ![]() nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space ...nitrate reductase (cytochrome) / nitrate reductase (cytochrome) activity / nitrate reductase activity / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / nitrate assimilation / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arnoux, P. / Sabaty, M. / Alric, J. / Frangioni, B. / Guigliarelli, B. / Adriano, J.-M. / Pignol, D. | ||||||
![]() | ![]() Title: Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase Authors: Arnoux, P. / Sabaty, M. / Alric, J. / Frangioni, B. / Guigliarelli, B. / Adriano, J.-M. / Pignol, D. #1: ![]() Title: The 1.25 A Resolution Structure of the Diheme Napb Subunit of Soluble Nitrate Reductase Reveals a Novel Cytochrome C Fold with a Stacked Heme Arrangement Authors: Brige, A. / Leys, D. / Meyer, T.E. / Cusanovich, M.A. / Van Beeumen, J.J. #2: ![]() Title: Crystal Structure of the First Dissimilatory Nitrate Reductase (Nap) at 1.9 A Solved by MAD Methods Authors: 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. | ||||||
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. THE SHEETS PRESENTED AS "CG" 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. THE SHEETS PRESENTED AS "EF" 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. THE SHEETS PRESENTED AS "GG" 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. THE SHEETS PRESENTED AS "IG" 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. THE SHEETS PRESENTED AS "KF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "OG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-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 | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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5 | ![]()
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6 | ![]()
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7 | ![]()
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8 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 2 types, 16 molecules ACEGIKMOBDFHJLNP
#1: Protein | Mass: 90114.625 Da / Num. of mol.: 8 / Fragment: CATALYTIC SUBUNIT, RESIDUES 30-831 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 14590.408 Da / Num. of mol.: 8 / Fragment: CYTOCHROME SUBUNIT, RESIDUES 25-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 48 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/MGD.gif)
![](data/chem/img/HEC.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-MO / #5: Chemical | ChemComp-MGD / #6: Chemical | ChemComp-HEC / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8.2 Details: VAPOUR-DIFFUSION. MIXING EQUAL AMOUNTS OF PROTEIN 25MG/ML., pH 8.20 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. obs: 134043 / % possible obs: 97.1 % / Redundancy: 2 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 30 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS Highest resolution: 3.2 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2NAP, 1JNI Resolution: 3.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE ARE 8 HETERODIMERS IN THE ASU BUT THE PHYSIOLOGICAL UNIT IS ONE HETERODIMER. RESTRAINTS HAD BEEN RELEASED IN THE LAST REFINEMENT STEP. HETERODIMER WITH CHAIN ID A AND B IS THE COMPLEX ...Details: THERE ARE 8 HETERODIMERS IN THE ASU BUT THE PHYSIOLOGICAL UNIT IS ONE HETERODIMER. RESTRAINTS HAD BEEN RELEASED IN THE LAST REFINEMENT STEP. HETERODIMER WITH CHAIN ID A AND B IS THE COMPLEX HAVING THE LOWEST TEMPERATURE FACTOR.
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Displacement parameters | Biso mean: 42.8 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.24 Å / Total num. of bins used: 26
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.269 / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |