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Yorodumi- PDB-4fcz: Crystal Structure of Toluene-tolerance protein from Pseudomonas p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fcz | ||||||
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Title | Crystal Structure of Toluene-tolerance protein from Pseudomonas putida (strain KT2440), Northeast Structural Genomics Consortium (NESG) Target PpR99 | ||||||
Components | Toluene-tolerance protein | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Tgt2/MlaC / Tgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Toluene tolerance protein Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å | ||||||
Authors | Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target PpR99 Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fcz.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fcz.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fcz ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fcz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | monomer,24.6 kD,88.3% |
-Components
#1: Protein | Mass: 25131.518 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: ttg2D, PP_0961 / References: UniProt: Q88P91 #2: 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: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Operator: l,-k,h / Fraction: 0.068 |
Reflection | Resolution: 2.6→39.086 Å / Num. obs: 28693 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.604→39.086 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0.13 / Phase error: 30.07 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.604→39.086 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.3534 Å / Origin y: 18.1984 Å / Origin z: 53.8285 Å
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Refinement TLS group |
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