+Open data
-Basic information
Entry | Database: PDB / ID: 1jp6 | ||||||
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Title | Sperm Whale met-Myoglobin (room temperature; room pressure) | ||||||
Components | myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT complex | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Urayama, P. / Gruner, S.M. / Phillips Jr., G.N. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Probing substates in sperm whale myoglobin using high-pressure crystallography. Authors: Urayama, P. / Phillips Jr., G.N. / Gruner, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jp6.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jp6.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jp6 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jp6 | HTTPS FTP |
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-Related structure data
Related structure data | 1jp8C 1jp9C 1jpbC 1vxhS C: citing same article (ref.) S: Starting model for refinement |
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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: 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 | #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.36 % / Description: 295K; 0.1MPa; pH6 |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 6 / Details: ammonium sulfate, pH 6, batch, temperature 298K |
Crystal grow | *PLUS Method: batch method / PH range low: 6 / PH range high: 5.5 |
Components of the solutions | *PLUS Conc.: 72-78 %sat / Common name: ammonium sulfate / Details: pH5.5-6.0 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Sep 8, 1997 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→9.2 Å / Num. all: 5870 / Num. obs: 5870 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 15.6 / Num. unique all: 825 / % possible all: 94.5 |
Reflection shell | *PLUS % possible obs: 94.5 % |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1VXH Resolution: 2.3→9.18 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 762440.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: residue 153 was disordered
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.7685 Å2 / ksol: 0.397049 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→9.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 9.2 Å / Num. reflection obs: 5853 / σ(F): 2 / % reflection Rfree: 10.9 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.166 |