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Yorodumi- PDB-1h29: Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Stru... -
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-Basic information
Entry | Database: PDB / ID: 1h29 | ||||||
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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 | ||||||
Components | HIGH-MOLECULAR-WEIGHT CYTOCHROME C | ||||||
Keywords | ELECTRON TRANSPORT / HIGH MOLECULAR MASS CYTOCHROME / SULFATE RESPIRATION / HYDROGEN CYCLE / TRANSMEMBRANE REDOX COMPLEX / ENERGY CONSERVATION / PROTON GRADIENT / TETRA-HEME / C3-LIKE DOMAIN | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO VULGARIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å | ||||||
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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h29.cif.gz | 464 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h29.ent.gz | 408.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h29 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h29 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 55765.961 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P24092 #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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9179 |
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
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Refinement | Method to determine structure: MAD / Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.051 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→30 Å
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