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Yorodumi- PDB-1cku: AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cku | ||||||
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Title | AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL IRON PROTEIN STRUCTURES AT ATOMIC RESOLUTION | ||||||
Components | PROTEIN (HIPIP) | ||||||
Keywords | ELECTRON TRANSFER PROTEIN / ATOMIC RESOLUTION / DIRECT METHODS / IRON-SULPHUR CLUSTER / METALLOPROTEIN | ||||||
Function / homology | Function and homology information aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Allochromatium vinosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.2 Å | ||||||
Authors | Parisini, E. / Capozzi, F. / Lubini, P. / Lamzin, V. / Luchinat, C. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution. Authors: Parisini, E. / Capozzi, F. / Lubini, P. / Lamzin, V. / Luchinat, C. / Sheldrick, G.M. #1: Journal: J.Biol.Chem. / Year: 1974 Title: Two-Angstrom Crystal Structure of Oxidized Chromatium High Potential Iron Protein Authors: Carter, C.W. / Kraut, J. / Freer, S.T. / Xuong, N.-H. / Alden, R.A. / Bartsch, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cku.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cku.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cku_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 1cku_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 1cku_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1cku_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1cku ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1cku | 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: (-0.75271, 0.64149, -0.14805), Vector: |
-Components
#1: Protein | Mass: 8912.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allochromatium vinosum (bacteria) / Strain: XL1BLUE / Plasmid: PLEHP20 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P00260 #2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 Details: 1.3 M AMMONIUM SULPHATE, 40 MM TRIS 180 MM KCL, pH 5.3 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 1997 / Details: BENT CRYSTAL |
Radiation | Monochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9091 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 50551 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.2→1.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.4 / % possible all: 94.4 |
Reflection | *PLUS Num. measured all: 636238 |
Reflection shell | *PLUS Rmerge(I) obs: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.2→20 Å / Num. parameters: 14394 / Num. restraintsaints: 17533 / Cross valid method: FREE R / σ(F): 0 StereochEM target val spec case: NO RESTRAINTS ON PROSTHETIC GROUPS (RESIDUE 87 IN CHAINS A AND B) Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 1182 / Occupancy sum non hydrogen: 1562.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.132 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.03 |