[English] 日本語
Yorodumi- PDB-1gnt: Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gnt | ||||||
---|---|---|---|---|---|---|---|
Title | Hybrid Cluster Protein from Desulfovibrio vulgaris. X-ray structure at 1.25A resolution using synchrotron radiation. | ||||||
Components | HYBRID CLUSTER PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / HYBRID CLUSTER PROTEIN / AEROBIC DESULFOVIBRIO VULGARIS | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO VULGARIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. ...Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2002 Title: Hybrid cluster proteins (HCPs) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at 1.25 A resolution using synchrotron radiation. Authors: Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / LeGall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gnt.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gnt.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 1gnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gnt_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gnt_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1gnt_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1gnt_validation.cif.gz | 51.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/1gnt ftp://data.pdbj.org/pub/pdb/validation_reports/gn/1gnt | HTTPS FTP |
-Related structure data
Related structure data | 1gn9C 1gnlC 1e2uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60042.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS406 Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH NCIMB8303 / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH NCIMB8303 / References: UniProt: P31101 |
---|---|
#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-FSO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 25-30% PEG 8000 0.1M MES PH 5.9, 0.2M MAGNESIUM ACETATE, T=277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: 1999 / Details: PLATINUM COATED FUSED QUARTZ MIRROR |
Radiation | Monochromator: SI(111) BENT TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→19.92 Å / Num. obs: 163543 / % possible obs: 94.6 % / Redundancy: 2.4 % / Rsym value: 0.063 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.25→1.34 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.331 / % possible all: 86.4 |
Reflection | *PLUS Num. measured all: 400513 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 86.4 % / Rmerge(I) obs: 0.331 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB FROM ENTRY 1E2U Resolution: 1.25→19.92 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.978 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→19.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|