[English] 日本語
![](img/lk-miru.gif)
- PDB-1h29: Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Stru... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h29 | ||||||
---|---|---|---|---|---|---|---|
Title | Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer | ||||||
![]() | HIGH-MOLECULAR-WEIGHT CYTOCHROME C | ||||||
![]() | ELECTRON TRANSPORT / HIGH MOLECULAR MASS CYTOCHROME / SULFATE RESPIRATION / HYDROGEN CYCLE / TRANSMEMBRANE REDOX COMPLEX / ENERGY CONSERVATION / PROTON GRADIENT / TETRA-HEME / C3-LIKE DOMAIN | ||||||
Function / homology | ![]() periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matias, P.M. / Coelho, A.V. / Valente, F.M.A. / Placido, D. / Legall, J. / Xavier, A.V. / Pereira, I.A.C. / Carrondo, M.A. | ||||||
![]() | ![]() Title: Sulfate Respiration in Desulfovibrio Vulgaris Hildenborough: Structure of the 16-Heme Cytochrome C Hmca at 2.5 A Resolution and a View of its Role in Transmembrane Electron Transfer Authors: Matias, P.M. / Coelho, A.V. / Valente, F.M.A. / Placido, D. / Legall, J. / Xavier, A.V. / Pereira, I.A.C. / Carrondo, M.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 464 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 408.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 56.3 KB | Display | |
Data in CIF | ![]() | 79.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55765.961 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | Compound details | FORM TRANSMEMBRANE PROTEIN COMPLEX TO AID ELECTRON FLOW TO AID ENZYMES THAT ARE INVOLVED IN THE ...FORM TRANSMEMBR | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 7.5 Details: EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY ...Details: EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY SOAKED IN THE SOLUTION. AFTER A FEW DAYS AT 4C, SMALL HEXAGONAL BIPYRAMIDS STARTED STARTED TO APPEAR AND REACHED THEIR MAXIMUM SIZE AFTER ONE WEEK. THE BEST CRYOCRYSTALLOGRAPHY CONDITIONS WERE OBTAINED BY SOAKING THESE CRYSTALS IN A CRYSTALLIZATION SOLUTION CONTAINING 7.5% MPD, pH 7.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 89606 / % possible obs: 91.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3 / % possible all: 84 |
Reflection shell | *PLUS % possible obs: 84 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: RESIDUE NUMBERING FOLLOWS THE COMPLET PRECURSOR SEQUENCE INCLUDING SIGNAL PEPTIDE. CHAIN A HAS MISSIN RESIDUES 32-37, 500-504 AND 544-545. CHAIN B HAS MISSING RESIDU 32-37, 500-504 AND 542- ...Details: RESIDUE NUMBERING FOLLOWS THE COMPLET PRECURSOR SEQUENCE INCLUDING SIGNAL PEPTIDE. CHAIN A HAS MISSIN RESIDUES 32-37, 500-504 AND 544-545. CHAIN B HAS MISSING RESIDU 32-37, 500-504 AND 542-545. CHAIN C HAS MISSING RESIDUES 32-37, 500-505 AND 545. CHAIN D HAS MISSING RESIDUES 32-37,283-285, 394-397,500-505 AND 543-545.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|