+Open data
-Basic information
Entry | Database: PDB / ID: 3ehm | ||||||
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Title | Structure of BT1043 | ||||||
Components | SusD homolog | ||||||
Keywords | SUGAR BINDING PROTEIN / SusD homolog / glycan binding / mucin O-glycan binding / tetratrico-peptide repeat | ||||||
Function / homology | Function and homology information SusD-like, tetratrico peptide repeats domain / SusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Koropatkin, N.M. / Smith, T.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Authors: Koropatkin, N. / Martens, E.C. / Gordon, J.I. / Smith, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ehm.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ehm.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ehm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ehm_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 3ehm_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 3ehm_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 3ehm_validation.cif.gz | 62.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/3ehm ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3ehm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60025.594 Da / Num. of mol.: 2 / Fragment: UNP residues 18-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_1043 / Plasmid: pET-28rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A8X4 #2: Chemical | ChemComp-EDO / | #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: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 277 K / pH: 9 Details: 6-7% polyethylene glycol 6000, 50 mM NaCl, 50mM 2-(cyclohexylamino)-ethanesulfonic acid (CHES), pH 9.0, batch/microseeding, temperature 277K |
-Data collection
Diffraction | Mean temperature: 150 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934, 0.97951, 0.97167 | ||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 30, 2006 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.94→50 Å / Num. all: 78668 / Num. obs: 78668 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.062 / Net I/σ(I): 32.2 | ||||||||||||
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.139 |
-Processing
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Refinement | Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 32.387 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.83 Å2 / Biso mean: 19.417 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Xplor file |
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