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- PDB-4ak1: Structure of BT4661, a SusE-like surface located polysaccharide b... -

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Basic information

Entry
Database: PDB / ID: 4ak1
TitleStructure of BT4661, a SusE-like surface located polysaccharide binding protein from the Bacteroides thetaiotaomicron heparin utilisation locus
ComponentsBT_4661
KeywordsHEPARIN-BINDING PROTEIN / HEPARAN SULPHATE
Function / homology
Function and homology information


SH3 type barrels. - #1270 / BT4661 domain 1 / Immunoglobulin-like - #2720 / Immunoglobulin-like - #2730 / BT4661-like / Surface glycan binding protein BT4661-like / Cadherins / SH3 type barrels. / Roll / Immunoglobulins ...SH3 type barrels. - #1270 / BT4661 domain 1 / Immunoglobulin-like - #2720 / Immunoglobulin-like - #2730 / BT4661-like / Surface glycan binding protein BT4661-like / Cadherins / SH3 type barrels. / Roll / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF4958 domain-containing protein
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLowe, E.C. / Basle, A. / Czjzek, M. / Thomas, S. / Murray, H. / Firbank, S.J. / Bolam, D.N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans.
Authors: Cartmell, A. / Lowe, E.C. / Basle, A. / Firbank, S.J. / Ndeh, D.A. / Murray, H. / Terrapon, N. / Lombard, V. / Henrissat, B. / Turnbull, J.E. / Czjzek, M. / Gilbert, H.J. / Bolam, D.N.
History
DepositionFeb 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 2.0Dec 12, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BT_4661
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7863
Polymers77,7401
Non-polymers462
Water11,241624
1
A: BT_4661
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)466,71618
Polymers466,4406
Non-polymers27612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation12_545x,x-y-1,-z+1/21
crystal symmetry operation10_555-y,-x,-z+1/21
Buried area16700 Å2
ΔGint-170.1 kcal/mol
Surface area175330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.620, 158.620, 137.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2183-

HOH

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Components

#1: Protein BT_4661


Mass: 77740.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q89YS0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 3.79 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growDetails: 18-23% PEG 3350, 350 MM NA SULFATE, BTP PH 8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.95→45.79 Å / Num. obs: 73908 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→137.37 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.404 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED ATOMS WERE REMOVED
RfactorNum. reflection% reflectionSelection details
Rfree0.24913 3716 5 %RANDOM
Rwork0.21578 ---
obs0.21745 70050 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.95→137.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 0 2 624 5203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9476459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55625.598209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79215734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5031512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213633
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 247 -
Rwork0.221 4778 -
obs--99.78 %
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)
16.46691.2452-3.86430.9149-1.02994.6386-0.27250.1893-0.431-0.04150.1034-0.03840.3277-0.10870.16910.0994-0.03940.04660.1899-0.04120.050282.748-79.40752.726
221.54161.1158-7.36759.1805-4.93254.7931-0.71950.7174-2.46970.19160.10620.24240.0885-0.25350.61340.5467-0.3980.57090.4002-0.36750.780265.137-98.46662.546
310.4383-0.8647-3.14480.10610.24671.0201-0.12040.0229-0.65790.0705-0.08390.18750.15870.04740.20430.4579-0.02090.45780.3706-0.0190.899598.513-102.44248.942
40.5872-0.09980.67950.2432-0.21531.2437-0.01270.0177-0.0880.03530.0480.00350.03330.0789-0.03540.06040.03580.01360.08710.01080.02399.646-65.926-1.685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 118
2X-RAY DIFFRACTION2A119 - 183
3X-RAY DIFFRACTION3A188 - 323
4X-RAY DIFFRACTION4A324 - 701

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