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Yorodumi- PDB-1hlb: Structural analysis of monomeric hemichrome and dimeric cyanomet ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hlb | ||||||
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Title | Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola | ||||||
Components | HEMOGLOBIN (DEOXY) | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Caudina arenicola (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Hackert, M.L. / Mitchell, D.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola. Authors: Mitchell, D.T. / Kitto, G.B. / Hackert, M.L. #1: Journal: J.Protein Chem. / Year: 1992 Title: Amino Acid Sequence of the Coelomic C Globin from the Sea Cucumber Caudina (Molpadia) Arenicola Authors: Mcdonald, G.D. / Davidson, L. / Kitto, G.B. #2: Journal: J.Biol.Chem. / Year: 1979 Title: Preliminary Crystallographic Data on Monomeric and Dimeric Hemoglobins from the Sea Cucumber, Molpadia Arenicola Authors: Carson, W.M. / Bowers, T.R. / Kitto, G.B. / Hackert, M.L. #3: Journal: Biochim.Biophys.Acta / Year: 1976 Title: Functional Consequences of Ligand-Linked Dissociation in Hemoglobin from the Sea Cucumber Molpadia Arenicola Authors: Bonaventura, C. / Bonaventura, J. / Kitto, B. / Brunori, M. / Antonini, E. #4: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 1976 Title: N-Terminal Substitution of Some Sea Cucumber Hemoglobins Authors: Kitto, G.B. / Erwin, D. / West, R. / Omnaas, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hlb.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hlb.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hlb ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hlb | HTTPS FTP |
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-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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Atom site foot note | 1: HEMICHROME COORDINATION OF HEME IRON ATOM WITH BOTH THE PROXIMAL AND DISTAL HISTIDINES COORDINATING TO THE HEME IRON ATOM. |
-Components
#1: Protein | Mass: 17584.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caudina arenicola (invertebrata) / References: UniProt: P80018 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: unknown / Details: Carson, W.M., (1979) J.Biol.Chem., 254, 7400. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 2.5→5 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.59 |