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Yorodumi- PDB-4n4u: Crystal structure of ABC transporter solute binding protein BB071... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n4u | ||||||
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Title | Crystal structure of ABC transporter solute binding protein BB0719 from Bordetella bronchiseptica RB50, TARGET EFI-510049 | ||||||
Components | Putative ABC transporter periplasmic solute-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / ABC PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å | ||||||
Authors | Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n4u.cif.gz | 254.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n4u.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n4u_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 4n4u_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 4n4u_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 4n4u_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n4u ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n4u | HTTPS FTP |
-Related structure data
Related structure data | 4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n6dC 4n6kC 4n8gC 4n8yC 4n91C 4napC 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 4oanC 4ovpC 4ovqC 4ovrC 4ovsC 4ovtC 4p1eC 4p1lC 4p3lC 4p47C 4p56C 4p8bC 4p9kC 4pafC 4paiC 4pakC 4pbhC 4pbqC 4pc9C 4pcdC 4pddC 4pdhC 4pe3C 4petC 4pf6C 4pf8C 4pfbC 4pfiC 4pfrC 4pgnC 4pgpC 4uabC C: citing same article (ref.) |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35600.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB0719 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WPG5, UniProt: A0A0H3LMU1*PLUS #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.23 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROTEIN IN 10 MM HEPES, PH 7.5, 150 MM SODIUM CHLORIDE, 5% GLYCEROL, RESERVOIR: 0.1M BIS-TRIS:HCL, 28% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2013 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 168537 / % possible obs: 99.5 % / Observed criterion σ(I): -5 / Redundancy: 5 % / Biso Wilson estimate: 20.18 Å2 / Rsym value: 0.065 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.8 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.95 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→50 Å
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Refine LS restraints |
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