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Yorodumi- PDB-5mba: BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mba | |||||||||
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Title | BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION | |||||||||
Components | MYOGLOBIN | |||||||||
Keywords | OXYGEN STORAGE | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding / extracellular region Similarity search - Function | |||||||||
Biological species | Aplysia limacina (slug sea hare) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | |||||||||
Authors | Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M. | |||||||||
Citation | Journal: J.Mol.Recog. / Year: 1991 Title: Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution. Authors: Mattevi, A. / Gatti, G. / Coda, A. / Rizzi, M. / Ascenzi, P. / Brunori, M. / Bolognesi, M. #1: Journal: Structure and Function of Invertebrate Oxygen Carriers Year: 1991 Title: Aplysia Limacina Myoglobin: Molecular Bases for Ligand Binding Authors: Bolognesi, M. / Frigerio, F. / Lionetti, C. / Rizzi, M. / Ascenzi, P. / Brunori, M. #2: Journal: J.Mol.Biol. / Year: 1989 Title: Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution Authors: Bolognesi, M. / Onesti, S. / Gatti, G. / Coda, A. / Ascenzi, P. / Brunori, M. #3: Journal: J.Mol.Biol. / Year: 1985 Title: Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution Authors: Bolognesi, M. / Coda, A. / Gatti, G. / Ascenzi, P. / Brunori, M. #4: Journal: J.Mol.Biol. / Year: 1982 Title: Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study Authors: Bolognesi, M. / Cannillo, E. / Ascenzi, P. / Giacometti, G.M. / Merli, A. / Brunori, M. #5: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1978 Title: The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution Authors: Bolognesi, M. / Cannillo, E. / Oberti, R. / Rossi, G. / Ungaretti, L. #6: Journal: Acta Crystallogr.,Sect.B / Year: 1978 Title: The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution Authors: Ungaretti, L. / Bolognesi, M. / Cannillo, E. / Oberti, R. / Rossi, G. #7: Journal: J.Mol.Biol. / Year: 1975 Title: Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina Authors: Blundell, T.L. / Brunori, M. / Curti, B. / Bolognesi, M. / Coda, A. / Fumagalli, M. / Ungaretti, L. #8: Journal: Int.J.Pept.Protein Res. / Year: 1973 Title: The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina Authors: Tentori, L. / Vivaldi, G. / Carta, S. / Marinucci, M. / Massa, A. / Antonini, E. / Brunori, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mba.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mba.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mba_validation.pdf.gz | 799.7 KB | Display | wwPDB validaton report |
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Full document | 5mba_full_validation.pdf.gz | 803.7 KB | Display | |
Data in XML | 5mba_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5mba_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mba ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mba | 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
#1: Protein | Mass: 15349.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia limacina (slug sea hare) / References: UniProt: P02210 |
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#2: Chemical | ChemComp-AZI / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | AZIDE ION IS BOUND TO THE HEME IRON AT THE DISTAL SITE AND TRIGGERS A LARGE CONFORMATIONAL CHANGE ...AZIDE ION IS BOUND TO THE HEME IRON AT THE DISTAL SITE AND TRIGGERS A LARGE CONFORMATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.94 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion / Details: took Bolognesi et al., from original paper | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.139 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 11 Å / Num. reflection obs: 7487 / Rfactor obs: 0.139 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 2.35 |