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Yorodumi- PDB-1a4a: AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a4a | ||||||
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Title | AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT 16 DEGREES CELSIUS | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT / CUPROPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Achromobacter denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Messerschmidt, A. / Prade, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH. Authors: Messerschmidt, A. / Prade, L. / Kroes, S.J. / Sanders-Loehr, J. / Huber, R. / Canters, G.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4a.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4a.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a4a_validation.pdf.gz | 372.6 KB | Display | wwPDB validaton report |
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Full document | 1a4a_full_validation.pdf.gz | 375.4 KB | Display | |
Data in XML | 1a4a_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1a4a_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4a ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4a | HTTPS FTP |
-Related structure data
Related structure data | 1a4bC 1a4cC 2azaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14004.870 Da / Num. of mol.: 2 / Mutation: M121H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter denitrificans (bacteria) / Cellular location: PERIPLASM / Gene: AZU / Plasmid: PCH11 / Gene (production host): AZU / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P00280 #2: Chemical | #3: Water | ChemComp-HOH / | 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: NO MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→13.96 Å / Num. obs: 21362 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.085 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.89→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.503 / % possible all: 75.8 |
Reflection | *PLUS Num. measured all: 75639 |
Reflection shell | *PLUS % possible obs: 75.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AZA Resolution: 1.89→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2.5
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Displacement parameters | Biso mean: 25.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.98 Å / Rfactor Rwork: 0.2872 / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Num. reflection obs: 1865 |