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- PDB-5mqn: Glycoside hydrolase BT_0986 -

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Basic information

Entry
Database: PDB / ID: 5mqn
TitleGlycoside hydrolase BT_0986
ComponentsGlycosyl hydrolases family 2, sugar binding domain
KeywordsHYDROLASE / glycoside hydrolase / rhamnosidase / plant pectin / CAZy family 106
Function / homologyalpha-L-rhamnosidase / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / DNA binding / metal ion binding / DNA-binding protein / Glycoside hydrolase family 2, sugar binding protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
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 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,2564
Polymers125,1361
Non-polymers1203
Water17,439968
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-35 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.291, 85.758, 120.870
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
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 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.9→49.17 Å / Num. all: 380421 / Num. obs: 101961 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4655 / CC1/2: 0.671 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDS5.8.0155data reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing
Cootmodel building
REFMACphasing
REFMAC5.8.0155refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.083 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20512 5016 4.9 %RANDOM
Rwork0.17388 ---
obs0.17543 96922 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.217 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.07 Å2
2---0.39 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8271 0 3 968 9242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198526
X-RAY DIFFRACTIONr_bond_other_d0.0020.028018
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.94911576
X-RAY DIFFRACTIONr_angle_other_deg0.954318481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43151049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73524.138406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.454151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.481556
X-RAY DIFFRACTIONr_chiral_restr0.0920.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021982
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_it0.5950.9334163
X-RAY DIFFRACTIONr_mcbond_other0.5950.9324162
X-RAY DIFFRACTIONr_mcangle_it1.0611.3945202
X-RAY DIFFRACTIONr_mcangle_other1.0611.3955203
X-RAY DIFFRACTIONr_scbond_it0.5960.9834363
X-RAY DIFFRACTIONr_scbond_other0.5960.9844364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0271.4466368
X-RAY DIFFRACTIONr_long_range_B_refined6.19312.0199826
X-RAY DIFFRACTIONr_long_range_B_other6.02310.8389529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 347 -
Rwork0.354 7204 -
obs--99.15 %
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)
10.3332-0.0679-0.3710.40410.22050.5351-0.0274-0.1897-0.0544-0.11660.0518-0.0492-0.01190.3904-0.02440.05230.01150.00150.5774-0.08860.071545.73231.87330.042
20.19080.0128-0.28741.29251.63432.7318-0.00510.0101-0.05030.10730.0854-0.0644-0.00510.1269-0.08030.2133-0.0314-0.01370.2893-0.05510.110427.68351.4857.049
30.18810.0912-0.11080.25910.22350.5820.05380.03780.0085-0.01930.03770.0283-0.11990.1052-0.09150.1599-0.02240.00960.3216-0.00650.126.96239.11824.783
41.09220.08451.04990.49390.46352.1730.07810.0291-0.20290.0384-0.03780.09830.4115-0.0577-0.04030.2959-0.0131-0.06740.2314-0.0370.179414.81-0.73827.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 190
2X-RAY DIFFRACTION2A191 - 299
3X-RAY DIFFRACTION3A300 - 922
4X-RAY DIFFRACTION4A947 - 1102

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