[English] 日本語
Yorodumi- PDB-1gm4: OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gm4 | ||||||
---|---|---|---|---|---|---|---|
Title | OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 at pH 7.6 | ||||||
Components | CYTOCHROME C3 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO DESULFURICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Bento, I. / Louro, R. / Matias, P.M. / Catarino, T. / Baptista, A.M. / Soares, C.M. / Carrondo, M.A. / Turner, D.L. / Xavier, A.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome. Authors: Louro, R.O. / Bento, I. / Matias, P.M. / Catarino, T. / Baptista, A.M. / Soares, C.M. / Carrondo, M.A. / Turner, D.L. / Xavier, A.V. #1: Journal: Inorg.Chim.Acta / Year: 1998 Title: Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstrom S Resolution Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A. #2: Journal: Biochemistry / Year: 1995 Title: Structure of the Tetraheme Cytochrome from Desulfovibrio Desulfuricans Atcc 27774: X-Ray Diffraction and Electron Paramagnetic Resonance Studies. Authors: Morais, J. / Palma, P.N. / Frazao, C. / Caldeira, J. / Legall, J. / Moura, I. / Moura, J.J. / Carrondo, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gm4.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gm4.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1gm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gm4 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gm4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gmbC 3cyrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11618.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q9L915 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
---|---|
Crystal grow | pH: 7.6 / Details: pH 7.60 |
Crystal grow | *PLUS Method: other / Details: Morais, J., (1995) Biochemistry, 34, 12830. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→24 Å / Num. obs: 7877 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5.28 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 23 Å / Num. obs: 7949 / Num. measured all: 62904 |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CYR Resolution: 2.05→24 Å / Cross valid method: FREE R-VALUE / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |