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Yorodumi- PDB-4xeq: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xeq | ||||||
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Title | CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (Deval_0042, TARGET EFI-510114) BOUND TO COPURIFIED (R)-PANTOIC ACID | ||||||
Components | TRAP dicarboxylate transporter, DctP subunit | ||||||
Keywords | TRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be published Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (Deval_0042, TARGET EFI-510114) BOUND TO COPURIFIED (R)-PANTOIC ACID Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xeq.cif.gz | 458.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xeq.ent.gz | 395.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xeq_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 4xeq_full_validation.pdf.gz | 483.4 KB | Display | |
Data in XML | 4xeq_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 4xeq_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/4xeq ftp://data.pdbj.org/pub/pdb/validation_reports/xe/4xeq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | biological unit is a monomer |
-Components
#1: Protein | Mass: 37319.715 Da / Num. of mol.: 4 / Fragment: UNP residues 37-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: RCH1 / Gene: Deval_0042 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3ILJ0, UniProt: A0A0E0SY65*PLUS #2: Chemical | ChemComp-PAF / #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: 2.07 Å3/Da / Density % sol: 40.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M di-Ammonium Citrate pH 5.0 , 20 %(w/v) PEG 3350); Cryoprotection (80% Reservoir + 20% Glycerol) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2014 / Details: MIRRORS | |||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection twin | Operator: h,-k,-l / Fraction: 0.4 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.7→25.26 Å / Num. obs: 131847 / % possible obs: 98.6 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.044 / Net I/σ(I): 12.2 / Num. measured all: 945105 / Scaling rejects: 109 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→25.254 Å / FOM work R set: 0.7488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.95 / 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 max: 60.09 Å2 / Biso mean: 18.84 Å2 / Biso min: 9.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→25.254 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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