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- PDB-2ww3: Structure of the Family GH92 Inverting Mannosidase BT3990 from Ba... -

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Basic information

Entry
Database: PDB / ID: 2ww3
TitleStructure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with thiomannobioside
ComponentsPUTATIVE ALPHA-1,2-MANNOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 92 / GH92 / BT3990
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / glycoprotein catabolic process / protein deglycosylation / protein quality control for misfolded or incompletely synthesized proteins / carbohydrate binding / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
GH92 mannosidase domain / GH92 mannosidase fold / alpha-1,2-mannosidase / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 ...GH92 mannosidase domain / GH92 mannosidase fold / alpha-1,2-mannosidase / Glycosyl hydrolase family fold / alpha-1,2-mannosidases domains / Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Six-hairpin glycosidase superfamily / Beta-galactosidase; Chain A, domain 5 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Distorted Sandwich / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside / Putative alpha-1,2-mannosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSuits, M.D.L. / Zhu, Y. / Thompson, A.J. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Mechanistic Insights Into a Ca(2+)-Dependent Family of Alpha-Mannosidases in a Human Gut Symbiont.
Authors: Zhu, Y. / Suits, M.D.L. / Thompson, A.J. / Chavan, S. / Dinev, Z. / Dumon, C. / Smith, N. / Moremen, K.W. / Xiang, Y. / Siriwardena, A. / Williams, S.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionOct 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ALPHA-1,2-MANNOSIDASE
B: PUTATIVE ALPHA-1,2-MANNOSIDASE
C: PUTATIVE ALPHA-1,2-MANNOSIDASE
D: PUTATIVE ALPHA-1,2-MANNOSIDASE
E: PUTATIVE ALPHA-1,2-MANNOSIDASE
F: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,89621
Polymers514,1456
Non-polymers2,75115
Water23,0771281
1
A: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1954
Polymers85,6911
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1033
Polymers85,6911
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1954
Polymers85,6911
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1033
Polymers85,6911
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1954
Polymers85,6911
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PUTATIVE ALPHA-1,2-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1033
Polymers85,6911
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.260, 68.590, 204.009
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PUTATIVE ALPHA-1,2-MANNOSIDASE / MANNOSIDASE


Mass: 85690.859 Da / Num. of mol.: 6 / Fragment: RESIDUES 20-755
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET 22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER / References: UniProt: Q8A0N1
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside / methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp2SH]{[(2+S)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1281 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO- ALPHA-D-MANNOPYRANOSIDE (SMD): ALPHA-1,2 SULPHUR LINKED ...METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO- ALPHA-D-MANNOPYRANOSIDE (SMD): ALPHA-1,2 SULPHUR LINKED MANNOBIOSE GLYCEROL (GOL): GLYCEROL WAS USED AS CRYOPROTECTANT
Sequence detailsFIRST 19 RESIDUES WERE REMOVED DURING CLONING

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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: 2.2 Å3/Da / Density % sol: 44.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 239524 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVX
Resolution: 2.1→203.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.377 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24366 12627 5 %RANDOM
Rwork0.18989 ---
obs0.1925 239524 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.262 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å2-2.31 Å2
2--1.57 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→203.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35677 0 168 1281 37126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02236923
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.93850141
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02654416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54324.3991898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95155789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.73315154
X-RAY DIFFRACTIONr_chiral_restr0.0820.25082
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02129116
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_it0.4861.521971
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.878235393
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.591314952
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.44.514747
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: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 845 -
Rwork0.288 16123 -
obs--89.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3507-0.1240.24370.207-0.12060.63880.0718-0.1009-0.0333-0.06340.05070.08420.07480.0298-0.12250.06290.0206-0.0380.0662-0.02510.1141-13.6577-66.0621155.4062
20.4923-0.34320.46380.502-0.12440.9228-0.00270.27220.0194-0.0844-0.08270.0162-0.1950.40920.08540.0946-0.04330.00770.25450.0150.002112.5035-40.5375129.2536
30.32470.07960.17420.17370.05690.50390.0020.11290.03440.00870.0294-0.02430.01680.0387-0.03140.0421-0.01630.01770.10230.02830.106742.3934-31.8858185.7187
40.13760.12020.27930.32080.07331.0794-0.0644-0.1042-0.04360.0332-0.004-0.0384-0.2831-0.35630.06840.090.0889-0.00230.1761-0.00550.045916.0085-6.377212.0586
50.3771-0.09870.27650.2849-0.09470.49110.0227-0.1085-0.02-0.05930.02780.1130.02250.0202-0.05050.04350.0163-0.01430.059-0.02490.154542.7285-66.611589.9303
60.2937-0.07510.27830.3203-0.07710.7636-0.06710.087-0.0018-0.0934-0.01190.0373-0.13820.23130.07910.1014-0.0327-0.00990.1102-0.00590.051766.0486-41.311660.8227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 755
2X-RAY DIFFRACTION2B20 - 755
3X-RAY DIFFRACTION3C20 - 755
4X-RAY DIFFRACTION4D20 - 755
5X-RAY DIFFRACTION5E20 - 755
6X-RAY DIFFRACTION6F20 - 755

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