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Yorodumi- PDB-2vqa: Protein-folding location can regulate Mn versus Cu- or Zn-binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqa | ||||||
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Title | Protein-folding location can regulate Mn versus Cu- or Zn-binding. Crystal Structure of MncA. | ||||||
Components | SLL1358 PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / METAL-BINDING PROTEIN / MN2+ / CUPIN / BI-CUPIN / OXALATE DECARBOXYLASE | ||||||
Function / homology | Function and homology information oxalate metabolic process / nutrient reservoir activity / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Tottey, S. / Waldron, K.J. / Firbank, S.J. / Reale, B. / Bessant, C. / Sato, K. / Gray, J. / Banfield, M.J. / Dennison, C. / Robinson, N.J. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Protein-Folding Location Can Regulate Manganese-Binding Versus Copper- or Zinc-Binding. Authors: Tottey, S. / Waldron, K.J. / Firbank, S.J. / Reale, B. / Bessant, C. / Sato, K. / Cheek, T.R. / Gray, J. / Banfield, M.J. / Dennison, C. / Robinson, N.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vqa.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqa.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqa ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqa | HTTPS FTP |
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-Related structure data
Related structure data | 1l3jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 39517.234 Da / Num. of mol.: 3 / Fragment: 35-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73510 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ACT / #4: 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: 4.2 Å3/Da / Density % sol: 70.5 % / Description: NONE |
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Crystal grow | pH: 4.2 / Details: 0.1M SODIUM ACETATE PH 3.25, 8% W/V PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→68.2 Å / Num. obs: 46724 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L3J Resolution: 2.95→58.32 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.719 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.303 / 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: 12.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→58.32 Å
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Refine LS restraints |
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