+Open data
-Basic information
Entry | Database: PDB / ID: 1bq8 | ||||||
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Title | Rubredoxin (Methionine Mutant) from Pyrococcus Furiosus | ||||||
Components | PROTEIN (RUBREDOXIN) | ||||||
Keywords | METAL BINDING PROTEIN / IRON-SULFUR PROTEIN / HIGH-RESOLUTION STRUCTURE | ||||||
Function / homology | Function and homology information alkane catabolic process / electron transfer activity / iron ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.1 Å | ||||||
Authors | Bau, R. / Rees, D.C. / Kurtz, D.M. / Scott, R.A. / Huang, H. / Adams, M.W.W. / Eidsness, M.K. | ||||||
Citation | Journal: J.BIOL.INORG.CHEM. / Year: 1998 Title: Crystal Structure of Rubredoxin from Pyrococcus Furiosus at 0.95 Angstroms Resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N- ...Title: Crystal Structure of Rubredoxin from Pyrococcus Furiosus at 0.95 Angstroms Resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability Authors: Bau, R. / Rees, D.C. / Kurtz, D.M. / Scott, R.A. / Huang, H. / Adams, M.W.W. / Eidsness, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bq8.cif.gz | 26.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bq8.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bq8_validation.pdf.gz | 382.2 KB | Display | wwPDB validaton report |
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Full document | 1bq8_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 1bq8_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1bq8_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bq8 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bq8 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6031.728 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: EXTRA MET IN N-TERMINUS / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Description: PRODUCT OF A SYNTHETIC PF RD GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P24297 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | IRON ATOM OF A FES4 UNIT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % / Description: KNOWN STRUCTURE (SEE TEXT) | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8.5 Details: VAPOR DIFFUSION AGAINST 3.6M NA,K PHOSPHATE, pH 8.5, vapor diffusion | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop / Details: used macroseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS X-1000 / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 45654 / % possible obs: 96.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.125 / % possible all: 87.2 |
Reflection | *PLUS Num. obs: 20698 / Num. measured all: 45654 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.1→50 Å / Num. parameters: 4541 / Num. restraintsaints: 4888 / σ(F): 0 Details: ANISOTROPIC C,N,O,S,FE B23 (A**2) : ESTIMATED OVERALL COORDINATE ERROR.
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Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.1 Å / σ(F): 0 / Num. reflection Rfree: 2041 / Rfactor Rwork: 0.119 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |