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Yorodumi- PDB-2aza: STRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aza | |||||||||
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Title | STRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT 1.8 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES | |||||||||
Components | AZURIN | |||||||||
Keywords | ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN) | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Achromobacter xylosoxidans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Baker, E.N. / Norris, G.E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1988 Title: Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules. Authors: Baker, E.N. #1: Journal: J.Am.Chem.Soc. / Year: 1986 Title: Blue Copper Proteins. The Copper Site in Azurin from Alcaligenes Denitrificans Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. #2: 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. #3: Journal: J.Mol.Biol. / Year: 1979 Title: Purification and Preliminary Crystallographic Studies on Azurin and Cytochrome C(Prime) 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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Remark 700 | SHEET STRAND 1 OF SHEET B1A (AND B1B) AND STRAND 1 OF SHEET B2A (AND B2B) ARE PARTS OF A PIECE OF ...SHEET STRAND 1 OF SHEET B1A (AND B1B) AND STRAND 1 OF SHEET B2A (AND B2B) ARE PARTS OF A PIECE OF EXTENDED CHAIN WHICH IS SPLIT BETWEEN BETWEEN THE TWO SHEETS. RESIDUES 14-16 BELONG TO SHEET B1 AND RESIDUES 18-22 BELONG TO SHEET B2 WITH A KINK IN BETWEEN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aza.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aza.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 2aza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aza_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 2aza_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 2aza_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2aza_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2aza ftp://data.pdbj.org/pub/pdb/validation_reports/az/2aza | 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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2 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 5. / 2: SEE REMARK 6. / 3: SEE REMARKS 5 AND 6. | |||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.10158, 0.99439, 0.02952), Vector: Details | THE TRANSFORMATION PROVIDED ON THE *MTRIX* RECORDS BELOW WILL PRODUCE APPROXIMATE COORDINATES FOR MOLECULE 1 (CHAIN INDICATOR *A*) WHEN APPLIED TO THE COORDINATES OF MOLECULE 2 (CHAIN INDICATOR *B*). | |
-Components
#1: Protein | Mass: 13997.919 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 | #4: Water | ChemComp-HOH / | Compound details | TURNS 3A AND 12A (AND 3B AND 12B) ARE MORE LIKE ALPHA-TURNS AS THEY HAVE GOOD 1-5 H-BONDS (O ALA 40 ...TURNS 3A AND 12A (AND 3B AND 12B) ARE MORE LIKE ALPHA-TURNS AS THEY HAVE GOOD 1-5 H-BONDS (O ALA 40 - N MET 44 AND O HIS 117 - N MET 121) WHICH ARE SHORTER THAN THE 1-4 H-BONDS (O ALA 40 - MET 43 AND 0 HIS 117 - N MET 120). | Sequence details | RESIDUE 42 IS INCLUDED HERE AS SER BOTH IN THE *ATOM* AND *SEQRES* RECORDS. RESIDUE 42 IS ALA IN ...RESIDUE 42 IS INCLUDED HERE AS SER BOTH IN THE *ATOM* AND *SEQRES* RECORDS. RESIDUE 42 IS ALA IN THE CHEMICALLY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % | |||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: other | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 21980 / % possible obs: 87 % |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 1.8 Å Details: ONLY INTERNAL H-BONDS INVOLVING SIDE CHAINS OR CROSSLINKING H BONDS BETWEEN STRANDS ARE PRESENTED ON THE CONECT RECORDS BELOW.
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Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor all: 0.157 / Num. reflection all: 21980 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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