+Open data
-Basic information
Entry | Database: PDB / ID: 1bqk | ||||||
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Title | OXIDIZED PSEUDOAZURIN | ||||||
Components | PSEUDOAZURIN | ||||||
Keywords | ELECTRON TRANSPORT / CUPROPROTEIN | ||||||
Function / homology | Function and homology information electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Achromobacter cycloclastes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Inoue, T. / Nishio, N. / Hamanaka, S. / Shimomura, T. / Harada, S. / Suzuki, S. / Kohzuma, T. / Shidara, S. / Iwasaki, H. / Kai, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of copper site in redox forms with the rearrangement of hydrogen bond ...Title: Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of copper site in redox forms with the rearrangement of hydrogen bond at a remote histidine. Authors: Inoue, T. / Nishio, N. / Suzuki, S. / Kataoka, K. / Kohzuma, T. / Kai, Y. #1: Journal: Thesis Title: Crystal Structure Determinations of Oxidized and Reduced Pseudoazurin from Achromobacter Cycloclastes: A Redox-Induced Conformational Change Contains a Peptide Bond Flip #2: Journal: J.Biochem.(Tokyo) / Year: 1993 Title: Crystallization and Preliminary X-Ray Studies on Pseudoazurin from Achromobacter Cycloclastes Iam1013 Authors: Inoue, T. / Nishio, N. / Kai, Y. / Harada, S. / Ohshiro, Y. / Suzuki, S. / Kohzuma, T. / Shidara, S. / Iwasaki, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bqk.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bqk.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bqk_validation.pdf.gz | 403.6 KB | Display | wwPDB validaton report |
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Full document | 1bqk_full_validation.pdf.gz | 403.8 KB | Display | |
Data in XML | 1bqk_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1bqk_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bqk ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bqk | HTTPS FTP |
-Related structure data
Related structure data | 1bqrC 1pzaS 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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Unit cell |
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-Components
#1: Protein | Mass: 13032.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OXIDIZED FORM OF PSEUDOAZURIN / Source: (natural) Achromobacter cycloclastes (bacteria) / Strain: IAM1013 / References: UniProt: P19567 |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 40 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Inoue, T., (1993) J.Biochem.(Tokyo), 114, 761. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 25, 1993 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→8 Å / Num. obs: 21303 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 9.02 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.182 / % possible all: 56 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 222685 |
Reflection shell | *PLUS Lowest resolution: 1.4 Å / % possible obs: 56 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZA Resolution: 1.35→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: ESTIMATED COORDINATE ERROR. ESD FROM LUZZATI PLOT (A) : 0.137
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Displacement parameters | Biso mean: 11.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |