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- PDB-5ck0: BT4246 -

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Basic information

Entry
Database: PDB / ID: 5ck0
TitleBT4246
ComponentsSusD homolog
Keywordsmucin-binding protein / SusD homologue / tetra-trico peptide repeat (TPR) / microbiota
Function / homology
Function and homology information


SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / NICKEL (II) ION / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
Model detailsmucin o-glycan binding SusD homologue
AuthorsKoropatkin, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Michigan Host Microbiome Initiative United States
CitationJournal: to be published
Title: Mechanistic insight into mucin degradation by the human gut microbiota reveals targeting of the glycoprotein core
Authors: Ndeh, D.A. / Nakjang, S. / Kwiatkowski, K.J. / Koropatkin, N.M. / Hirt, R.P. / Bolam, D.N.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6276
Polymers71,3731
Non-polymers2545
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-20 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.216, 156.216, 114.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-1351-

HOH

21A-1395-

HOH

31A-1418-

HOH

41A-1499-

HOH

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Components

#1: Protein SusD homolog


Mass: 71372.930 Da / Num. of mol.: 1 / Fragment: UNP residues 40-642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4246 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q89ZX5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG 3350, KCl / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.996→46.23 Å / Num. all: 55908 / Num. obs: 55908 / % possible obs: 99.25 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.2025 / Net I/σ(I): 8.03
Reflection shellResolution: 1.996→2.068 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.66 / % possible all: 96.63

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Semet structure

Resolution: 1.996→46.228 Å / FOM work R set: 0.8411 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2000 3.58 %random selection
Rwork0.1867 53887 --
obs0.1881 55887 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.6 Å2 / Biso mean: 13.15 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.996→46.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 5 699 5565
Biso mean--25.08 19.38 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075007
X-RAY DIFFRACTIONf_angle_d0.9726819
X-RAY DIFFRACTIONf_chiral_restr0.041699
X-RAY DIFFRACTIONf_plane_restr0.005891
X-RAY DIFFRACTIONf_dihedral_angle_d12.9511782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9962-2.04610.32471340.25493620375495
2.0461-2.10150.27181420.24273800394299
2.1015-2.16330.25481410.230738073948100
2.1633-2.23310.27061410.213937973938100
2.2331-2.31290.25321420.205138163958100
2.3129-2.40550.2441410.192738203961100
2.4055-2.5150.22051430.195538363979100
2.515-2.64760.2211420.193138423984100
2.6476-2.81350.23341420.187138303972100
2.8135-3.03060.23771440.191538724016100
3.0306-3.33550.24511430.18143869401299
3.3355-3.8180.20641450.16643896404199
3.818-4.80950.16521460.14773940408699
4.8095-46.24080.20161540.16624142429699

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