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- PDB-7m1b: SusE-like protein BT2857 -

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Basic information

Entry
Database: PDB / ID: 7m1b
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) / Galactose-binding-like domain superfamily / Galactose-binding-like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,2422
Polymers43,1801
Non-polymers621
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint3 kcal/mol
Surface area12550 Å2
Unit cell
Length a, b, c (Å)74.650, 48.790, 112.660
Angle α, β, γ (deg.)90.000, 103.602, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-672-

HOH

21AAA-794-

HOH

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Components

#1: Protein Galactose-binding-like protein / BT3158


Mass: 43179.773 Da / Num. of mol.: 1 / Fragment: UNP residues 21-402
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_3158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A2Z7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% w/v PEG4000, 8.0% v/v ethylene glycol, 0.4 M magnesium chloride, 100 mM Tris:HCl, pH 8.5

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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 PILATUS 6M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→40.5 Å / Num. obs: 63258 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 9179 / CC1/2: 0.939 / Rpim(I) all: 0.193 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7M1A

7m1a


Resolution: 1.5→40.487 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.761 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2368 3163 5 %
Rwork0.2007 60093 -
all0.203 --
obs-63256 99.913 %
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: 28.879 Å2
Baniso -1Baniso -2Baniso -3
1-1.098 Å20 Å20.473 Å2
2---2.217 Å20 Å2
3---0.797 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 4 229 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122231
X-RAY DIFFRACTIONr_angle_refined_deg1.921.6383030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52922.823124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3611510
X-RAY DIFFRACTIONr_chiral_restr0.1480.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021759
X-RAY DIFFRACTIONr_nbd_refined0.2050.2962
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2173
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.211
X-RAY DIFFRACTIONr_mcbond_it4.2022.5491062
X-RAY DIFFRACTIONr_mcangle_it4.2923.8141324
X-RAY DIFFRACTIONr_scbond_it5.7642.8981169
X-RAY DIFFRACTIONr_scangle_it5.8524.2161706
X-RAY DIFFRACTIONr_lrange_it5.56735.4273447
X-RAY DIFFRACTIONr_rigid_bond_restr9.60632231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.252330.21244270.21446670.8740.89199.850.186
1.539-1.5810.2292250.18642820.18945130.8940.90899.86710.162
1.581-1.6270.2062190.17441640.17643870.9150.9299.90880.147
1.627-1.6770.242150.16940740.17242930.9020.93299.90680.143
1.677-1.7320.2062070.16639380.16841470.9240.93599.95180.139
1.732-1.7920.1932010.1638260.16140310.9260.94199.90080.136
1.792-1.860.2221950.15136930.15438910.920.94299.92290.133
1.86-1.9360.1771880.15535690.15637570.9460.9471000.141
1.936-2.0210.1991780.16633830.16835650.9280.94199.88780.157
2.021-2.120.2071730.17132980.17334730.9370.94599.94240.164
2.12-2.2340.231610.18130610.18332240.9070.93499.9380.178
2.234-2.3690.2371540.18629110.18930700.9230.93799.83710.188
2.369-2.5320.2431460.18527780.18829270.9270.94499.89750.193
2.532-2.7340.2031350.19125700.19227050.9450.941000.203
2.734-2.9940.2381260.20723960.20925220.9220.931000.225
2.994-3.3450.2461130.20421370.20622520.9210.9499.91120.235
3.345-3.8580.2291010.20219210.20320230.9280.94399.95060.24
3.858-4.7140.252860.21716360.21917230.9240.93799.9420.276
4.714-6.6220.336670.27412790.27713460.910.9121000.353
6.622-40.4870.317400.3447500.3437930.8770.89299.62170.479

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