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Yorodumi- PDB-2xl7: Structure and metal-loading of a soluble periplasm cupro-protein:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xl7 | ||||||
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Title | Structure and metal-loading of a soluble periplasm cupro-protein: Cu- CucA-closed (SeMet) | ||||||
Components | SLL1785 PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / CUPIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SYNECHOCYSTIS SP. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Waldron, K.J. / Firbank, S.J. / Dainty, S.J. / Perez-Rama, M. / Tottey, S. / Robinson, N.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure and Metal Loading of a Soluble Periplasm Cuproprotein. Authors: Waldron, K.J. / Firbank, S.J. / Dainty, S.J. / Perez-Rama, M. / Tottey, S. / Robinson, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xl7.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xl7.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xl7 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xl7 | HTTPS FTP |
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-Related structure data
Related structure data | 2xl9SC 2xlaC 2xlfC 2xlgC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27305.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. PCC 6803 (bacteria) / Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P73600 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-URE / | #4: Chemical | ChemComp-CL / | #5: 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: 3.87 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 20% (W/V) PEG 8000, 0.5MM CUSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→60 Å / Num. obs: 18072 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XL9 Resolution: 2.4→44.24 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.986 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.312 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→44.24 Å
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Refine LS restraints |
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