+Open data
-Basic information
Entry | Database: PDB / ID: 2xwk | ||||||
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Title | SiaP R147A mutant in complex with Neu5Ac | ||||||
Components | SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP | ||||||
Keywords | TRANSPORT PROTEIN / PERIPLASMIC BINDING PROTEIN / TRAP TRANSPORTER / SUGAR TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HAEMOPHILUS INFLUENZAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Fischer, M. / Hubbard, R.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Tripartite ATP-Independent Periplasmic (Trap) Transporters Use an Arginine-Mediated Selectivity Filter for High Affinity Substrate Binding. Authors: Fischer, M. / Hopkins, A.P. / Severi, E. / Hawkhead, J. / Bawdon, D. / Watts, A.G. / Hubbard, R.E. / Thomas, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xwk.cif.gz | 158.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xwk.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xwk_validation.pdf.gz | 803.7 KB | Display | wwPDB validaton report |
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Full document | 2xwk_full_validation.pdf.gz | 804.4 KB | Display | |
Data in XML | 2xwk_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2xwk_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/2xwk ftp://data.pdbj.org/pub/pdb/validation_reports/xw/2xwk | HTTPS FTP |
-Related structure data
Related structure data | 2xwiC 2xwoC 2xwvC 2v4cS 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
#1: Protein | Mass: 34946.504 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS PAH16 / References: UniProt: P44542 |
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#2: Sugar | ChemComp-SLB / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 7 Details: 35 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, 15 MM NEU5AC, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0 28.5% PEG 6K,100MM SODIUM MALONATE (PH 7.0)); TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→28.36 Å / Num. obs: 51332 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 7.3 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V4C Resolution: 1.49→28.36 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.221 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.062 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.529 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→28.36 Å
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Refine LS restraints |
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