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- PDB-4ufc: Crystal structure of the GH95 enzyme BACOVA_03438 -

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Basic information

Entry
Database: PDB / ID: 4ufc
TitleCrystal structure of the GH95 enzyme BACOVA_03438
ComponentsGH95
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / XYLAN / ALPHA-L-GALACTOSIDASE / GUT MICROBIOTA
Function / homology
Function and homology information


alpha-L-fucosidase activity / metal ion binding
Similarity search - Function
Alpha-L-fucosidase / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / putative glycoside hydrolase family protein from bacillus halodurans / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / beta-L-galactopyranose / Glyco_hyd_65N_2 domain-containing protein
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsRogowski, A. / Briggs, J.A. / Mortimer, J.C. / Tryfona, T. / Terrapon, N. / Lowe, E.C. / Basle, A. / Morland, C. / Day, A.M. / Zheng, H. ...Rogowski, A. / Briggs, J.A. / Mortimer, J.C. / Tryfona, T. / Terrapon, N. / Lowe, E.C. / Basle, A. / Morland, C. / Day, A.M. / Zheng, H. / Rogers, T.E. / Thompson, P. / Hawkins, A.R. / Yadav, M.P. / Henrissat, B. / Martens, E.C. / Dupree, P. / Gilbert, H.J. / Bolam, D.N.
CitationJournal: Nat.Commun. / Year: 2015
Title: Glycan Complexity Dictates Microbial Resource Allocation in the Large Intestine.
Authors: Rogowski, A. / Briggs, J.A. / Mortimer, J.C. / Tryfona, T. / Terrapon, N. / Lowe, E.C. / Basle, A. / Morland, C. / Day, A.M. / Zheng, H. / Rogers, T.E. / Thompson, P. / Hawkins, A.R. / ...Authors: Rogowski, A. / Briggs, J.A. / Mortimer, J.C. / Tryfona, T. / Terrapon, N. / Lowe, E.C. / Basle, A. / Morland, C. / Day, A.M. / Zheng, H. / Rogers, T.E. / Thompson, P. / Hawkins, A.R. / Yadav, M.P. / Henrissat, B. / Martens, E.C. / Dupree, P. / Gilbert, H.J. / Bolam, D.N.
History
DepositionMar 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: GH95
B: GH95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,8459
Polymers183,0912
Non-polymers7557
Water0
1
A: GH95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9034
Polymers91,5451
Non-polymers3573
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9435
Polymers91,5451
Non-polymers3974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.692, 179.117, 205.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GH95


Mass: 91545.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7M011
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GIV / beta-L-galactopyranose / beta-L-galactose / L-galactose / galactose / Galactose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-galactopyranoseCOMMON NAMEGMML 1.0
b-L-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 160 MM CALCIUM ACETATE 80 MM SODIUM CACODYLATE PH 6.5 14.4 % (W/V) POLYETHYLENE GLYCOL 8000 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.81→49.31 Å / Num. obs: 48329 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.81→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RDY

2rdy


Resolution: 2.81→134.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 31.68 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22805 2439 5.1 %RANDOM
Rwork0.18636 ---
obs0.18849 45776 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---2.95 Å20 Å2
3---3.49 Å2
Refinement stepCycle: LAST / Resolution: 2.81→134.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12531 0 37 0 12568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912890
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212025
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.93817528
X-RAY DIFFRACTIONr_angle_other_deg0.945327633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52351573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71124.712624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.667152111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621558
X-RAY DIFFRACTIONr_chiral_restr0.080.21891
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114785
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023105
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_it0.6861.3626298
X-RAY DIFFRACTIONr_mcbond_other0.6861.3626297
X-RAY DIFFRACTIONr_mcangle_it1.2032.0417869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8591.4136592
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: 2.808→2.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 137 -
Rwork0.348 2249 -
obs--67.14 %
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)
10.27360.3619-0.38810.7107-0.60161.27370.0360.07810.17790.12540.04030.1577-0.08540.055-0.07620.08750.02320.01440.32610.05090.543918.931204.64113.745
20.35530.1562-0.09661.3091-0.72670.4522-0.02410.080.0936-0.0714-0.0577-0.1768-0.00220.04850.08190.04620.0220.01510.36720.08080.506333.064209.808-0.376
30.16480.2332-0.12890.582-0.22890.4643-0.03360.02930.02360.02140.01470.05540.05270.03810.01890.13110.04120.02350.32270.02010.530218.692183.47114.007
41.0134-1.15222.46311.803-3.05416.12020.251-0.1364-0.29090.11590.2515-0.01260.4207-0.3739-0.50250.51680.0675-0.11150.0685-0.01020.796129.123161.2778.649
51.82270.9233-1.59661.6126-0.30861.6894-0.34530.0778-0.2101-0.03820.19020.05690.44520.02120.15520.1970.08020.01530.2525-0.01120.436618.987164.3126.984
60.26630.4779-0.11121.8921-0.04740.6095-0.0029-0.16210.04490.187-0.1356-0.05680.06250.09520.13850.09980.040.03690.31030.01770.48073.942138.78255.166
70.64620.3096-0.33792.66210.05780.5058-0.0199-0.18490.05130.2349-0.063-0.4329-0.06470.13240.08290.058-0.0299-0.11490.36220.02070.521620.495152.95561.111
80.24740.1286-0.14280.6587-0.18190.4389-0.1185-0.02320.0317-0.126-0.0514-0.11550.1011-0.04780.16990.16330.02080.13890.31310.0340.50964.206133.56835.414
93.855-1.79083.48541.4474-0.95344.03170.22240.4257-0.64090.0012-0.06220.45540.53740.435-0.16010.43860.02280.37440.2698-0.13070.534713.555127.49813.012
101.32080.9348-0.04881.50780.33320.9783-0.26590.3642-0.0264-0.69790.0667-0.11370.2468-0.06970.19910.62960.06240.24990.18930.05060.29464.117131.35615.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 133
2X-RAY DIFFRACTION2A134 - 328
3X-RAY DIFFRACTION3A329 - 749
4X-RAY DIFFRACTION4A750 - 768
5X-RAY DIFFRACTION5A769 - 807
6X-RAY DIFFRACTION6B20 - 133
7X-RAY DIFFRACTION7B134 - 286
8X-RAY DIFFRACTION8B287 - 750
9X-RAY DIFFRACTION9B751 - 768
10X-RAY DIFFRACTION10B769 - 807

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