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- PDB-5mqm: Glycoside hydrolase BT_0986 -

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Basic information

Entry
Database: PDB / ID: 5mqm
TitleGlycoside hydrolase BT_0986
ComponentsGlycosyl hydrolases family 2, sugar binding domain
KeywordsHYDROLASE / glycoside hydrolase / rhamnosidase / plant pectin / CAZy family 106
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / DNA binding / metal ion binding
Similarity search - Function
alpha-L-rhamnosidase / : / Glycosyl hydrolase 2 galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / D-rhamnopyranose tetrazole / DNA-binding protein / Glycoside hydrolase family 2, sugar binding protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
iotechnology and Biological Research CouncilBB/K020358/1 United Kingdom
iotechnology and Biological Research CouncilBB/K001949/1 United Kingdom
Wellcome TrustWT097907MA United Kingdom
European Research Council322820 United Kingdom
CitationJournal: Nature / Year: 2017
Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.
Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Aug 23, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 1, 2024Group: 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

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Assembly

Deposited unit
A: Glycosyl hydrolases family 2, sugar binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1319
Polymers125,1361
Non-polymers9958
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area39890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.050, 84.810, 120.630
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycosyl hydrolases family 2, sugar binding domain / BT_0986


Mass: 125135.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: Btheta7330_02599 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FM19, UniProt: Q8A931*PLUS

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-RPQ / D-rhamnopyranose tetrazole


Mass: 186.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N4O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG 550 MME, 15% (w/v) PEG 20000, 0.25 M rahmnose, 50mM hepes and 50 mm MOPS pH 7.56 6mM D-rhamnopyranose tetrazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→50.69 Å / Num. obs: 75602 / % possible obs: 98.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.9
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.548 / % possible all: 98.9

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Processing

Software
NameVersionClassification
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo model

Resolution: 2.11→50.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.428 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24026 3563 4.9 %RANDOM
Rwork0.1986 ---
obs0.20064 69011 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.332 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å2-1.24 Å2
2--0.48 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 2.11→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 62 323 8656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198545
X-RAY DIFFRACTIONr_bond_other_d0.0020.028041
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.95311574
X-RAY DIFFRACTIONr_angle_other_deg0.954318532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63151037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17524.109404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.113151430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5651556
X-RAY DIFFRACTIONr_chiral_restr0.0860.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021975
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_it1.3363.3184151
X-RAY DIFFRACTIONr_mcbond_other1.3353.3174150
X-RAY DIFFRACTIONr_mcangle_it2.1934.9695184
X-RAY DIFFRACTIONr_mcangle_other2.1934.975185
X-RAY DIFFRACTIONr_scbond_it1.5493.5164394
X-RAY DIFFRACTIONr_scbond_other1.5493.5164394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5955.1846390
X-RAY DIFFRACTIONr_long_range_B_refined3.98437.2479268
X-RAY DIFFRACTIONr_long_range_B_other3.98437.2529269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 276 -
Rwork0.282 5114 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 28.4162 Å / Origin y: 33.8568 Å / Origin z: 29.4694 Å
111213212223313233
T0.0573 Å20.003 Å2-0.0412 Å2-0.025 Å20.0032 Å2--0.0416 Å2
L0.1487 °20.0139 °2-0.0333 °2-0.2656 °20.1939 °2--0.3803 °2
S0.013 Å °0.0518 Å °0.0202 Å °0.0284 Å °0.0301 Å °-0.0163 Å °0.003 Å °0.039 Å °-0.0431 Å °

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