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Yorodumi- PDB-1hbg: GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hbg | ||||||
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Title | GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION | ||||||
Components | HEMOGLOBIN (CARBONMONOXY) | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Glycera dibranchiata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Arents, G.A. / Braden, B.C. / Padlan, E.A. / Love, W.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Glycera dibranchiata hemoglobin. Structure and refinement at 1.5 A resolution. Authors: Arents, G. / Love, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hbg.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hbg.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 1hbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/1hbg ftp://data.pdbj.org/pub/pdb/validation_reports/hb/1hbg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SEVEN RESIDUES HAVE THEIR SIDE CHAINS MODELED IN MORE THAN ONE CONFORMATION. THEY ARE LEU 31, MET 79, LYS 84, ASN 95, SER 109, SER 112, AND SER 143. ALSO SEE REMARK 6 ABOVE. |
-Components
#1: Protein | Mass: 14935.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycera dibranchiata (invertebrata) / References: UniProt: P02216 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CMO / |
#4: Water | ChemComp-HOH / |
Sequence details | THERE ARE A NUMBER OF SEQUENCE DIFFERENCES BETWEEN THE SEQUENCE PRESENTED IN THIS ENTRY AND THAT IN ...THERE ARE A NUMBER OF SEQUENCE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.52 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: unknown / Details: took Padlan & Love (1974) from original paper | ||||||||||||||||||||||||
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 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Num. obs: 15951 / Observed criterion σ(I): 1.5 / Num. measured all: 39770 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.146 / Highest resolution: 1.5 Å Details: LEUCINE 31 SHOWS EQUAL WEIGHT FOR EACH OF THE THREE POSSIBLE GAUCHE CONFORMATIONS OF ATOMS CD1 AND CD2. THESE ARE PRESENTED AS THREE ALTERNATE CONFORMATIONS WITH AN OCCUPANCY OF 0.33 EACH. ...Details: LEUCINE 31 SHOWS EQUAL WEIGHT FOR EACH OF THE THREE POSSIBLE GAUCHE CONFORMATIONS OF ATOMS CD1 AND CD2. THESE ARE PRESENTED AS THREE ALTERNATE CONFORMATIONS WITH AN OCCUPANCY OF 0.33 EACH. NOTE THAT ONLY THREE SETS OF COORDINATES WERE USED TO MODEL THIS DISORDER AND, THEREFORE, THE SIX ATOMS APPEAR AS THREE ATOMS IN A GRAPHICAL VIEW OF THE ENTRY. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor obs: 0.146 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |