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- PDB-6zj6: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 6zj6
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine
ComponentsGlycosyl hydrolase family 71
KeywordsHYDROLASE / mannosidase / retaining
Function / homologyGlycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / hydrolase activity, acting on glycosyl bonds / membrane / ACETATE ION / alpha-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / methylcyclohexane / Glycosyl hydrolase family 71
Function and homology information
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsThompson, A.J. / Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Thompson, A.J. / Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 5items
OrganizationGrant numberCountry
European Research Council (ERC)322942 United Kingdom
Australian Research Council (ARC)DP120101396 Australia
Australian Research Council (ARC)FT130100103 Australia
Australian Research Council (ARC)DP180101957 Australia
Biotechnology and Biological Sciences Research Council (BBSRC)BB/G016127/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.
Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
History
DepositionJun 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jan 20, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_related_exp_data_set / struct_conn
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Glycosyl hydrolase family 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6669
Polymers43,9341
Non-polymers7338
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint24 kcal/mol
Surface area14700 Å2
Unit cell
Length a, b, c (Å)107.981, 107.981, 67.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11AAA-610-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein Glycosyl hydrolase family 71


Mass: 43933.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria)
Gene: BXY_34140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 470 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-QTE / methylcyclohexane / Methylcyclohexane


Mass: 98.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 3 M sodium acetate pH 6.6 - 7,4 / PH range: 6.6-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.09→76.35 Å / Num. obs: 153951 / % possible obs: 95.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.027 / Rrim(I) all: 0.065 / Χ2: 0.78 / Net I/σ(I): 12.5
Reflection shellResolution: 1.09→1.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5269 / CC1/2: 0.358 / Rpim(I) all: 0.715 / Rrim(I) all: 1.342 / Χ2: 0.43 / % possible all: 66.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia20.5.902-gffa11588-dials-1.14data reduction
Aimless0.7.4data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HMG

6hmg


Resolution: 1.09→76.35 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.839 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1355 7638 4.961 %
Rwork0.1133 146308 -
all0.114 --
obs-153946 95.856 %
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: 17.312 Å2
Baniso -1Baniso -2Baniso -3
1-0.098 Å2-0 Å2-0 Å2
2--0.098 Å2-0 Å2
3----0.196 Å2
Refinement stepCycle: LAST / Resolution: 1.09→76.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 48 463 3417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133377
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173021
X-RAY DIFFRACTIONr_angle_refined_deg1.931.674658
X-RAY DIFFRACTIONr_angle_other_deg1.5661.5757093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84222.116189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751521
X-RAY DIFFRACTIONr_chiral_restr0.120.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02776
X-RAY DIFFRACTIONr_nbd_refined0.2270.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22878
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21607
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1010.21429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.216
X-RAY DIFFRACTIONr_nbd_other0.1940.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.234
X-RAY DIFFRACTIONr_mcbond_it2.3521.5931544
X-RAY DIFFRACTIONr_mcbond_other2.3511.5921545
X-RAY DIFFRACTIONr_mcangle_it2.8552.3991953
X-RAY DIFFRACTIONr_mcangle_other2.8642.4031954
X-RAY DIFFRACTIONr_scbond_it4.241.7791832
X-RAY DIFFRACTIONr_scbond_other4.241.7791832
X-RAY DIFFRACTIONr_scangle_it4.1182.5792660
X-RAY DIFFRACTIONr_scangle_other4.1182.5792661
X-RAY DIFFRACTIONr_lrange_it4.26819.6884108
X-RAY DIFFRACTIONr_lrange_other3.92918.7544000
X-RAY DIFFRACTIONr_rigid_bond_restr4.73736397
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
1.09-1.1180.2913800.27377050.274118340.7220.74868.32010.27
1.118-1.1490.234640.23388430.233115180.8550.85280.8040.225
1.149-1.1820.2165470.196100940.197112700.8910.89894.41880.184
1.182-1.2190.1715110.163103570.163108680.9360.9371000.151
1.219-1.2590.1675270.142100490.144105760.9450.9521000.127
1.259-1.3030.1544890.12997670.13102570.9550.9699.99020.112
1.303-1.3520.1385030.11293360.11398400.9670.97199.98980.095
1.352-1.4070.1354840.09790010.09994850.9730.9781000.083
1.407-1.470.1114480.08186820.08291300.9820.9861000.07
1.47-1.5410.1084480.07682780.07887290.9840.98899.96560.068
1.541-1.6250.1034210.0778560.07282770.9860.9891000.065
1.625-1.7230.1023710.06774940.06878650.9870.9911000.064
1.723-1.8420.0973570.07169890.07273590.9880.99199.82330.072
1.842-1.990.1183370.08665590.08868960.9830.9871000.092
1.99-2.1790.1323330.09659830.09863160.980.9851000.109
2.179-2.4360.1232820.10154660.10257480.9830.9851000.119
2.436-2.8130.1482600.11647940.11850590.9760.98199.90120.143
2.813-3.4440.1412160.12840840.12943000.9740.9781000.163
3.444-4.8650.1231700.12131820.12133560.9830.98399.88080.161
4.865-76.3540.173900.15217890.15318800.9680.9799.94680.207

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