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- PDB-7m1a: SusE-like protein BT2857 -

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Basic information

Entry
Database: PDB / ID: 7m1a
TitleSusE-like protein BT2857
ComponentsGalactose-binding like protein
KeywordsSUGAR BINDING PROTEIN / SusE-like / Galactose / Bacteroides thetaiotaomicron
Function / homologyDomain of unknown function DUF5000 / Domain of unknown function DUF4959 / Domain of unknown function DUF5126 / Domain of unknown function (DUF4959) / Domain of unknown function / Domain of unknown function (DUF5126) / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Galactose-binding like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsSuits, M.D.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05018 Canada
CitationJournal: Front Microbiol / Year: 2021
Title: Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family.
Authors: Stevenson, J. / Ngo, M. / Brandt, A. / Weadge, J.T. / Suits, M.D.L.
History
DepositionMar 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Galactose-binding like protein
BBB: Galactose-binding like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,10312
Polymers41,5272
Non-polymers57710
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint5 kcal/mol
Surface area15590 Å2
Unit cell
Length a, b, c (Å)59.300, 61.080, 61.760
Angle α, β, γ (deg.)90.000, 101.587, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Galactose-binding like protein / BT2857


Mass: 20763.324 Da / Num. of mol.: 2 / Fragment: UNP residues 221-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2857 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A3U7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 6.0% w/v PEG3350, 5% v/v ethylene glycol, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.42→46.87 Å / Num. obs: 81091 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Net I/σ(I): 15.6
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.231 / Num. unique obs: 11501 / CC1/2: 0.956 / Rpim(I) all: 0.14 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.42→43.021 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.819 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.199 3810 4.698 %
Rwork0.1669 77280 -
all0.168 --
obs-81090 99.481 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.172 Å20 Å2-0.229 Å2
2--0.425 Å20 Å2
3----0.146 Å2
Refinement stepCycle: LAST / Resolution: 1.42→43.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 34 403 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122944
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.6483970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4222.805164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2631518
X-RAY DIFFRACTIONr_chiral_restr0.1430.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022282
X-RAY DIFFRACTIONr_nbd_refined0.2160.21413
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2281
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5450.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.7750.221
X-RAY DIFFRACTIONr_mcbond_it8.8280.9861414
X-RAY DIFFRACTIONr_mcangle_it7.9921.4921764
X-RAY DIFFRACTIONr_scbond_it3.0521.2421530
X-RAY DIFFRACTIONr_scangle_it7.7271.7642206
X-RAY DIFFRACTIONr_lrange_it5.78415.5454748
X-RAY DIFFRACTIONr_rigid_bond_restr6.42932944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4570.2012670.165390X-RAY DIFFRACTION95.0437
1.457-1.4970.2032530.1455588X-RAY DIFFRACTION99.5908
1.497-1.540.1922820.1315379X-RAY DIFFRACTION99.683
1.54-1.5880.192800.1225240X-RAY DIFFRACTION99.729
1.588-1.640.1872540.1215107X-RAY DIFFRACTION99.7767
1.64-1.6970.1852530.124946X-RAY DIFFRACTION99.8655
1.697-1.7610.1832030.134755X-RAY DIFFRACTION99.9194
1.761-1.8330.1872110.1344597X-RAY DIFFRACTION99.9376
1.833-1.9140.1872410.1464414X-RAY DIFFRACTION99.8927
1.914-2.0080.1831950.1534205X-RAY DIFFRACTION99.8638
2.008-2.1160.2041830.174044X-RAY DIFFRACTION99.9055
2.116-2.2440.2132000.1713773X-RAY DIFFRACTION99.8994
2.244-2.3990.1911720.1763563X-RAY DIFFRACTION99.8663
2.399-2.5910.1931760.1663318X-RAY DIFFRACTION99.8571
2.591-2.8380.1931390.183096X-RAY DIFFRACTION99.9691
2.838-3.1720.2151380.1952765X-RAY DIFFRACTION100
3.172-3.6610.1991190.1922464X-RAY DIFFRACTION99.8454
3.661-4.4790.1651110.1842084X-RAY DIFFRACTION99.7274
4.479-6.3180.268810.2031626X-RAY DIFFRACTION99.9415
6.318-43.0210.296520.299926X-RAY DIFFRACTION99.6942

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