+Open data
-Basic information
Entry | Database: PDB / ID: 1duk | ||||||
---|---|---|---|---|---|---|---|
Title | WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN | ||||||
Components | WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Oxygen-storage protein / myoglobin / heme protein / 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: 2.13 Å | ||||||
Authors | Barrick, D. / Dahlquist, F.W. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Trans-substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion. Authors: Barrick, D. / Dahlquist, F.W. #1: Journal: To be Published Title: Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery Authors: Barrick, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1duk.cif.gz | 44 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1duk.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1duk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1duk ftp://data.pdbj.org/pub/pdb/validation_reports/du/1duk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FERRIC PROTOPORPHYRIN IX BOUND DURING BACTERIAL EXPRESSION OF THE PROTEIN Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: PMB413B / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop Details: 35 % PEG 8000, 0.3 M NaOAc, 0.1 M PIPES, VAPOR DIFFUSION, HANGING DROP Temp details: Room temperature | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Ambient temp details: Room temperature |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Feb 11, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. all: 7405 / Num. obs: 7405 / % possible obs: 78 % / Redundancy: 2.21 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.74 |
Reflection shell | Resolution: 2.13→2.29 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.163 / Num. unique all: 838 / % possible all: 47 |
Reflection shell | *PLUS % possible obs: 47 % |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.13→20 Å Stereochemistry target values: Bond lengths 0.02 rms; bond angles 3 degrees rms, trig planes 0.02 rms; general planes 0.02 rms; B-correlation 6.0 square angstroms rms.
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→20 Å
| ||||||||||||
Refine LS restraints |
|