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Yorodumi- PDB-1f6h: COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF A PROTEIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f6h | ||||||
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Title | COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF A PROTEIN | ||||||
Components | MYOGLOBIN (MET) | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / POWDER DIFFRACTION / RIETVELD REFINEMENT / MYOBLOBIN(MET) / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | POWDER DIFFRACTION / SYNCHROTRON / Resolution: 3.31 Å | ||||||
Authors | Von Dreele, R.B. | ||||||
Citation | Journal: J.APPL.CRYSTALLOGR. / Year: 1999 Title: Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure Authors: Von Dreele, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f6h.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f6h.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f6h_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 1f6h_full_validation.pdf.gz | 486.3 KB | Display | |
Data in XML | 1f6h_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1f6h_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f6h ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f6h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: POWDER DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.15 % / Description: SECOND PHASE OF (NH4)2SO4 IN SAMPLE | ||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: grinding / pH: 6.37 Details: saturated ammonium sulphate, sodium dihydrogen phosphate, dipotassium phosphate, powder slurry in 1.5mm capillary, 4mm long, pH 6.37, grinding, temperature 300K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 1.14991 |
Detector | Detector: SCINTILLATOR / Date: Mar 20, 1998 / Details: 2MM X 8MM BEAM ANALYZER : GE(111) |
Radiation | Monochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Wavelength: 1.14991 Å / Relative weight: 1 |
Reflection | Resolution: 3.31→47.06 Å / Num. all: 2088 / Num. obs: 2088 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % |
-Processing
Software |
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Refinement | Resolution: 3.31→47.06 Å / σ(F): 0 Stereochemistry target values: Engh & Huber bonds and angles, peptide planes, aromatic planes, minimum van der Waals contacts, H-bond contacts, torsion angle pseudopotentials Details: powder pattern Rwp=0.0230, Rp=0.0168, Nobs=4648 powder profile points
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Refinement step | Cycle: LAST / Resolution: 3.31→47.06 Å
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Refine LS restraints |
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Software | *PLUS Name: GSAS / Classification: refinement | ||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_chiral_restr / Dev ideal: 0.153 |