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- PDB-5ck1: selenomethionine BT4246 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ck1
Titleselenomethionine BT4246
ComponentsSusD homolog
Keywordsmucin-binding protein / SusD homologue / tetra-trico peptide repeat (TPR) / microbiota
Function / homologySusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / metal ion binding / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.835 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)73,9015
Polymers73,6751
Non-polymers2264
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-4 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.792, 115.738, 116.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1604-

HOH

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Components

#1: Protein SusD homolog


Mass: 73674.531 Da / Num. of mol.: 1 / Fragment: UNP residues 26-642
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG3350, KCl, nucleation off of a grain of SiO2. / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / 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: 1.835→31.83 Å / Num. all: 65430 / Num. obs: 65430 / % possible obs: 99.66 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1095 / Net I/σ(I): 37.41
Reflection shellResolution: 1.835→1.901 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 13.3 / % possible all: 98.08

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 1.835→31.827 Å / FOM work R set: 0.8683 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1998 3.06 %random selection
Rwork0.1671 63363 --
obs0.1682 65361 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.63 Å2 / Biso mean: 19.62 Å2 / Biso min: 2.77 Å2
Refinement stepCycle: final / Resolution: 1.835→31.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 19 819 5568
Biso mean--22.35 30.36 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064905
X-RAY DIFFRACTIONf_angle_d0.9256669
X-RAY DIFFRACTIONf_chiral_restr0.037678
X-RAY DIFFRACTIONf_plane_restr0.004869
X-RAY DIFFRACTIONf_dihedral_angle_d12.8961744
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 (%)
1.8352-1.88110.26511250.20114374449997
1.8811-1.93190.26081550.186444844639100
1.9319-1.98880.22511350.18144924627100
1.9888-2.0530.2151400.170945064646100
2.053-2.12630.2071430.16444604603100
2.1263-2.21140.17921490.1745144663100
2.2114-2.31210.21311390.16645104649100
2.3121-2.43390.21161460.169445214667100
2.4339-2.58630.22991400.17545454685100
2.5863-2.78590.24981390.177345424681100
2.7859-3.06610.16751460.171445434689100
3.0661-3.50930.22081460.16545704716100
3.5093-4.41940.15051420.145146134755100
4.4194-31.83170.19091530.16474689484299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0031-0.00460.0017-0.0026-0.00310.0001-0.04190.01470.0184-0.0077-0.017-0.0112-0.0230.002400.03410.0423-0.0595-0.03340.041-0.003691.452346.200558.071
2-0.00160.0002-0.00280.0006-0.0008-0.0009-0.0126-0.02370.01680.0201-0.0140.0016-0.0203-0.010200.06730.0598-0.0795-0.03410.02620.063889.766855.832477.9771
30.0012-0.0010.0019-0.0045-0.0020.0018-0.0351-0.01620.01940.0193-0.01740.0032-0.03270.00430-0.0930.0504-0.1227-0.01310.0486-0.091798.501544.893477.7334
40.00850.01120.00550.01630.00810.0346-0.0075-0.0239-0.0044-0.0041-0.01440.0002-0.0002-0.048700.05510.016-0.00930.0663-0.0110.053479.463128.901660.5045
50.00360.0017-0.00610.0044-0.01020.0084-0.01090.0156-0.0077-0.0021-0.0201-0.0057-0.02770.0222-00.0456-0.001-0.00580.0520.00630.041199.447935.314853.5432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 104 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 158 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 250 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 576 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 577 through 642 )A0

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