+Open data
-Basic information
Entry | Database: PDB / ID: 1cno | ||||||
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Title | STRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD | ||||||
Components | CYTOCHROME C552 | ||||||
Keywords | ELECTRON TRANSPORT / PSEUDOMONAS NAUTICA / X RAY STRUCTURE / MULTIWAVELENGTH ANOMALOUS DISPERSION / HEME / CYTOCHROME C | ||||||
Function / homology | Function and homology information periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Marinobacter hydrocarbonoclasticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Brown, K. / Nurizzo, D. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association. Authors: Brown, K. / Nurizzo, D. / Besson, S. / Shepard, W. / Moura, J. / Moura, I. / Tegoni, M. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cno.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cno.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cno_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 1cno_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 1cno_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 1cno_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/1cno ftp://data.pdbj.org/pub/pdb/validation_reports/cn/1cno | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 8710.734 Da / Num. of mol.: 8 / Source method: isolated from a natural source Details: C HEME IN EACH MONOMER LINKED BY CYS 14 AND 17 AND HIS 18 AND MET 60 AS AXIAL LIGANDS Source: (natural) Marinobacter hydrocarbonoclasticus (bacteria) Cellular location: PERIPLASM / Strain: 617 / References: UniProt: P82903 #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 ...THE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 CHANGED TO LYS 36; GLY 79 CHANGED TO TYR 79 COMPARED TO REF. EURO. J. BIOL. (1994), 224, 1011-1017. | |
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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: 4.36 Å3/Da / Density % sol: 72 % Description: THE STARTING MODEL WAS THE C552 FROM PS. NAUTICA SOLVED BY MAD METHOD AT 2.8A RESOLUTION | ||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
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: ESRF / Beamline: ID09 / Wavelength: 0.756 |
Detector | Type: THOMPSON Detector: X RAY IMAGE INTENSIFIER (THOMPSON) + PRINCETON CCD DETECTOR Date: May 1, 1998 / Details: FOCUSED BEAM TOROIDAL |
Radiation | Monochromator: LAUE BRAGG / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.756 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 58183 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 18.84 Å2 / Rsym value: 0.108 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.246 / % possible all: 94.3 |
Reflection | *PLUS Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS Rmerge(I) obs: 0.229 |
-Processing
Software |
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Refinement | Resolution: 2.2→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 400000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 19.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 2.2 Å / Luzzati sigma a obs: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2083 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.267 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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