+Open data
-Basic information
Entry | Database: PDB / ID: 1nwp | ||||||
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Title | CRYSTALLOGRAPHIC STUDY OF AZURIN FROM PSEUDOMONAS PUTIDA | ||||||
Components | AZURIN | ||||||
Keywords | ELECTRON TRANSPORT / CUPREDOXIN / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mathews, F.S. / Chen, Z.-W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallographic study of azurin from Pseudomonas putida. Authors: Chen, Z.W. / Barber, M.J. / McIntire, W.S. / Mathews, F.S. #1: Journal: Arch.Biochem.Biophys. / Year: 1993 Title: The Amino Acid Sequence of Pseudomonas Putida Azurin Authors: Barber, M.J. / Trimboli, A.J. / Mcintire, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nwp.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nwp.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nwp_validation.pdf.gz | 414.3 KB | Display | wwPDB validaton report |
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Full document | 1nwp_full_validation.pdf.gz | 414.7 KB | Display | |
Data in XML | 1nwp_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1nwp_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nwp ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nwp | HTTPS FTP |
-Related structure data
Related structure data | 1nwoC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13737.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: NCIB 9869 / References: UniProt: P34097 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 38.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP METHOD AT 4 C BY MIXING 5 MICROLITER PROTEIN AT 10- 15MG PER ML WITH PEG8000 SOLUTION CONTAINING 5MM TRIS-HCL BUFFER, PH 5 MICROLITER 30-36% 6.5-7.5 ,100MM NACL AND 180MM ZINC ...Details: HANGING DROP METHOD AT 4 C BY MIXING 5 MICROLITER PROTEIN AT 10- 15MG PER ML WITH PEG8000 SOLUTION CONTAINING 5MM TRIS-HCL BUFFER, PH 5 MICROLITER 30-36% 6.5-7.5 ,100MM NACL AND 180MM ZINC ACETATE., pH 7.0, vapor diffusion - hanging drop, temperature 277K PH range: 6.5-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1992 / Details: CU KA RADIATION |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 27846 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.6→1.72 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 1.9 / % possible all: 78 |
Reflection | *PLUS Num. measured all: 241088 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AZURIN FROM ALCALIGENES DENITRIFICANS (ENTRY NO. 2AZA) Resolution: 1.6→10 Å / σ(F): 1.5
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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