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Yorodumi- PDB-5fjd: APO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fjd | |||||||||
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Title | APO-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORIUM OB3B | |||||||||
Components | COPPER STORAGE PROTEIN 1 | |||||||||
Keywords | COPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE | |||||||||
Function / homology | Twin-arginine translocation signal, Cys-rich four helix bundle protein / metal ion binding / Copper storage protein 1 Function and homology information | |||||||||
Biological species | METHYLOSINUS TRICHOSPORIUM OB3B (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Vita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Crombie, A.T. / Murrell, J.C. / Waldron, K.J. / Dennison, C. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: A Four-Helix Bundle Stores Copper for Methane Oxidation. Authors: Vita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Waldron, K.J. / Dennison, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjd.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjd.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjd ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjd | HTTPS FTP |
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-Related structure data
Related structure data | 5fjeC 5ajf C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 12609.529 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOSINUS TRICHOSPORIUM OB3B (bacteria) Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL60*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS, PH 6.5, 25% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.95 Å / Num. obs: 60896 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AJF 5ajf Resolution: 1.5→52.96 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.152 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→52.96 Å
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Refine LS restraints |
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