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Yorodumi- PDB-1kr7: Crystal structure of the nerve tissue mini-hemoglobin from the ne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kr7 | ||||||
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Title | Crystal structure of the nerve tissue mini-hemoglobin from the nemertean worm Cerebratulus lacteus | ||||||
Components | Neural globin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / nerve tissue / mini-hemoglobin / protein cavities / Oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Cerebratulus lacteus (milky ribbon-worm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Pesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray analysis of neural hemoglobin from the nemertean worm Cerebratulus lacteus Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Ascenzi, P. / Riggs, A.F. / Yamauchi, K. / Geuens, E. / Moens, L. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kr7.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kr7.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kr7_validation.pdf.gz | 834.8 KB | Display | wwPDB validaton report |
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Full document | 1kr7_full_validation.pdf.gz | 835.7 KB | Display | |
Data in XML | 1kr7_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1kr7_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1kr7 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1kr7 | 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11546.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm) Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: O76242 |
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-Non-polymers , 5 types, 110 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-HEM / |
#5: Chemical | ChemComp-OXY / |
#6: 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: 2.3 Å3/Da / Density % sol: 46.5 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.739, 1.740, 0.915 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 311 channel and Si 111 channel cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→35 Å / Num. all: 17906 / Num. obs: 17906 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.3 | ||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1168 / Rsym value: 0.239 / % possible all: 95.7 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Num. measured all: 67606 / Rmerge(I) obs: 0.054 | ||||||||||||
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.239 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→35.14 Å / SU B: 2.82431 / SU ML: 0.04376 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08727 / ESU R Free: 0.07211 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→35.14 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Rfactor all: 0.1563 / Rfactor obs: 0.153 / Rfactor Rfree: 0.18702 / Rfactor Rwork: 0.15298 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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