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Yorodumi- PDB-1azb: STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1azb | ||||||
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Title | STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT(COPPER) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Achromobacter xylosoxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Baker, E.N. / Shepard, W.E.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution. Authors: Shepard, W.E. / Kingston, R.L. / Anderson, B.F. / Baker, E.N. #1: Journal: J.Am.Chem.Soc. / Year: 1990 Title: Copper Coordination Geometry in Azurin Undergoes Minimal Change on Reduction of Copper(II) to Copper (I) Authors: Shepard, W.E.B. / Anderson, B.F. / Lewandoski, D.A. / Norris, G.E. / Baker, E.N. #2: Journal: J.Mol.Biol. / Year: 1988 Title: Structure of Azurin from Alcaligenes Denitrificans Refinement at 1.8 Angstroms Resolution and Comparison of the Two Crystallographically Independent Molecules Authors: Baker, E.N. #3: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Azurin from Alcaligenes Denitrificans at 2.5 Angstroms Resolution Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. #4: Journal: J.Mol.Biol. / Year: 1979 Title: Purification and Preliminary Crystallographic Studies on Azurin and Cytochrome C' from Alcaligenes Denitrificans and Alcaligenes Sp. Ncib 11015 Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. / Rumball, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1azb.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azb.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1azb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azb_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 1azb_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 1azb_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1azb_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azb ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.118, 0.993, 0.024), Vector: Details | THE ASYMMETRIC UNIT CONTAINS TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES, A AND B, RELATED BY AN APPROXIMATE TWO-FOLD AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR FOR MOLECULE A WHEN APPLIED TO MOLECULE B. | |
-Components
#1: Protein | Mass: 14008.003 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter xylosoxidans (bacteria) / References: UniProt: P00280 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | AMINO ACID SEQUENCE IS AS IN C.W.G. HOITINK, L.P. WOUDT, J.C.M. TURENHOUT, M. VAN DE KAMP, G.W. ...AMINO ACID SEQUENCE IS AS IN C.W.G. HOITINK, L.P. WOUDT, J.C.M. TURENHOUT, M. VAN DE KAMP, G.W. CARTERS (1990) GENE 90, 15-20. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: interface diffusion | |||||||||||||||||||||||||
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: 2.2 Å / Num. obs: 16203 / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→10 Å / Rfactor obs: 0.158 / σ(F): 0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. reflection all: 16003 / σ(F): 0 / Rfactor all: 0.158 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.047 |