+Open data
-Basic information
Entry | Database: PDB / ID: 1a7v | ||||||
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Title | CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS | ||||||
Components | CYTOCHROME C' | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shibata, N. / Iba, S. / Misaki, S. / Meyer, T.E. / Bartsch, R.G. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure. Authors: Shibata, N. / Iba, S. / Misaki, S. / Meyer, T.E. / Bartsch, R.G. / Cusanovich, M.A. / Morimoto, Y. / Higuchi, Y. / Yasuoka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a7v.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a7v.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1a7v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1a7v_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1a7v_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7v ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7v | HTTPS FTP |
-Related structure data
Related structure data | 2ccyS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997291, 0.046599, 0.056917), Vector: |
-Components
#1: Protein | Mass: 13152.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: P00149 #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: 2.23 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||
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 | Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 10513 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 2.1 / % possible all: 63 |
Reflection | *PLUS Num. measured all: 39136 |
Reflection shell | *PLUS % possible obs: 62.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCY Resolution: 2.3→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev Biso : 2 Å2 / Rms dev position: 0.1 Å / Weight Biso : 4.8 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.243 |