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- PDB-4c1s: Glycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 4c1s
TitleGlycoside hydrolase family 76 (mannosidase) Bt3792 from Bacteroides thetaiotaomicron VPI-5482
ComponentsGLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
KeywordsHYDROLASE / GUT MICROBIOTA
Function / homologyGlycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / catalytic activity / Mainly Alpha / Putative alpha-1,6-mannanase
Function and homology information
Biological speciesBACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. ...Cuskin, F. / Lowe, E.C. / Zhu, Y. / Temple, M. / Thompson, A.J. / Cartmell, A. / Piens, K. / Bracke, D. / Vervecken, W. / Munoz-Munoz, J.L. / Suits, M.D.L. / Boraston, A.B. / Williams, S.J. / Davies, G.J. / Abbott, W.D. / Martens, E.C. / Gilbert, H.J.
CitationJournal: Nature / Year: 2015
Title: Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.
Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, ...Authors: Cuskin, F. / Lowe, E.C. / Temple, M.J. / Zhu, Y. / Cameron, E.A. / Pudlo, N.A. / Porter, N.T. / Urs, K. / Thompson, A.J. / Cartmell, A. / Rogowski, A. / Hamilton, B.S. / Chen, R. / Tolbert, T.J. / Piens, K. / Bracke, D. / Vervecken, W. / Hakki, Z. / Speciale, G. / Munoz-Munoz, J.L. / Day, A. / Pena, M.J. / Mclean, R. / Suits, M.D. / Boraston, A.B. / Atherly, T. / Ziemer, C.J. / Williams, S.J. / Davies, G.J. / Abbott, D.W. / Martens, E.C. / Gilbert, H.J.
History
DepositionAug 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Mar 4, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
B: GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,85217
Polymers86,8612
Non-polymers99115
Water5,170287
1
A: GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,08111
Polymers43,4311
Non-polymers65110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7716
Polymers43,4311
Non-polymers3405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.100, 44.420, 103.050
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCOSIDE HYDROLASE FAMILY 76 MANNOSIDASE


Mass: 43430.590 Da / Num. of mol.: 2 / Fragment: ENZYMATIC FRAGMENT, RESIDUES 155-525
Source method: isolated from a genetically manipulated source
Details: BT3792 GENE FRAGMENT ENCODING RESIDUES 155- 514
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON VPI-5482 (bacteria)
Gene: BT3792 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8A174, mannan endo-1,6-alpha-mannosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8
Details: BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 ...Details: BT3792 AT A 20 MG PER ML BUFFERED IN IN 25 MM TRIS-HCL (PH 8.0), 500 MM NACL, 2 MM DTT WITH A RESERVOIR SOLUTION CONSISTING OF 5% GLYCEROL (V/V), 24% (W PER V) POLYETHYLENE GLYCOL 2,000 MONOMETHYL ETHER, 0.25 M SODIUM ACETATE, AND BIS-TRIS-HCL (PH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98005
DetectorType: MARRESEARCH MX-300HE / Detector: CCD / Date: Sep 14, 2012
Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) , TOROIDAL FOCUSING MIRROR (RH AND PT)
RadiationMonochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98005 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 52497 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K7X

3k7x


Resolution: 2.1→48.03 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.911 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25264 2674 5.1 %RANDOM
Rwork0.21359 ---
obs0.2156 49817 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.111 Å2
Baniso -1Baniso -2Baniso -3
1-12.47 Å20 Å2-21.1 Å2
2---13.73 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 64 287 6429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9338507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24324.006327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.706151019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6481535
X-RAY DIFFRACTIONr_chiral_restr0.1170.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024909
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_it2.4252.3082998
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2523.4573745
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0712.4633304
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 167 -
Rwork0.234 3666 -
obs--99.66 %

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