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- PDB-1gnl: Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray str... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gnl | |||||||||
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Title | Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A | |||||||||
![]() | HYBRID CLUSTER PROTEIN | |||||||||
![]() | HYBRID CLUSTER PROTEIN / ANAEROBIC DESULFOVIBRIO DESULFURICANS / IRON ANOMALOUS | |||||||||
Function / homology | ![]() hydroxylamine reductase / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.2 KB | Display | ![]() |
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PDB format | ![]() | 199.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gn9SC ![]() 1gntC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58595.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS399 Source: (natural) ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6 / Details: 25% PEG 4000, 0.1M MES PH6.0, T=277K, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.6 / Method: vapor diffusion, sitting 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: May 15, 2001 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→28.63 Å / Num. obs: 247243 / % possible obs: 94.9 % / Redundancy: 3.7 % / Rsym value: 0.054 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.215 / % possible all: 85.3 |
Reflection | *PLUS Num. measured all: 915955 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 85.3 % / Rmerge(I) obs: 0.215 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB FROM ENTRY 1GN9 Resolution: 1.25→28.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.672 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→28.63 Å
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Refine LS restraints |
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