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- PDB-5swi: Crystal structure of SpGH92 in complex with mannose -

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Basic information

Entry
Database: PDB / ID: 5swi
TitleCrystal structure of SpGH92 in complex with mannose
ComponentsSugar hydrolase
KeywordsHYDROLASE / Beta sandwich / (alpha/alpha)6 barrel / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate binding / carbohydrate metabolic process / hydrolase activity / metal ion binding
Similarity search - Function
Alpha-1,2-mannosidase, putative / Glycosyl hydrolase family 92 / Glycosyl hydrolase family 92 N-terminal domain / Glycosyl hydrolase family 92 catalytic domain / Glycosyl hydrolase family 92 N-terminal domain / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Alpha-mannosidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsShapiro-Ward, S. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 130305 Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence.
Authors: Robb, M. / Hobbs, J.K. / Woodiga, S.A. / Shapiro-Ward, S. / Suits, M.D. / McGregor, N. / Brumer, H. / Yesilkaya, H. / King, S.J. / Boraston, A.B.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sugar hydrolase
A: Sugar hydrolase
C: Sugar hydrolase
D: Sugar hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,66028
Polymers326,3054
Non-polymers2,35424
Water24,5721364
1
B: Sugar hydrolase
D: Sugar hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,23813
Polymers163,1532
Non-polymers1,08511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-41 kcal/mol
Surface area45870 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-117 kcal/mol
Surface area87200 Å2
MethodPISA
3
A: Sugar hydrolase
C: Sugar hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,42215
Polymers163,1532
Non-polymers1,26913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-40 kcal/mol
Surface area45590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.003, 161.711, 208.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROBA2 - 69225 - 715
21PROPROAB2 - 69225 - 715
12SERSERBA2 - 69325 - 716
22SERSERCC2 - 69325 - 716
13HISHISBA2 - 69425 - 717
23HISHISDD2 - 69425 - 717
14SERSERAB2 - 69325 - 716
24SERSERCC2 - 69325 - 716
15SERSERAB2 - 69325 - 716
25SERSERDD2 - 69325 - 716
16PROPROCC2 - 69225 - 715
26PROPRODD2 - 69225 - 715

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Sugar hydrolase


Mass: 81576.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: ERS003549_00384, ERS409165_00851, ERS409372_00266, ERS455085_01031, ERS515225_01644
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0Y0HIE3
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1364 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.25 M (NH4)2SO4, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97531 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97531 Å / Relative weight: 1
ReflectionResolution: 2.15→127.76 Å / Num. obs: 237386 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVY

2wvy


Resolution: 2.15→127.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.1722 / FOM work R set: 0.8167 / SU B: 5.311 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1821 / SU Rfree: 0.1563 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 11855 5 %RANDOM
Rwork0.1968 ---
obs0.198 225381 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.57 Å2 / Biso mean: 35.789 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.15→127.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21913 0 148 1364 23425
Biso mean--45.38 36.56 -
Num. residues----2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01922764
X-RAY DIFFRACTIONr_bond_other_d0.0040.0220474
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.94830970
X-RAY DIFFRACTIONr_angle_other_deg0.94347186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22552756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22924.181110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.383153518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.341597
X-RAY DIFFRACTIONr_chiral_restr0.0760.23326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125998
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025563
X-RAY DIFFRACTIONr_mcbond_it2.053.49611024
X-RAY DIFFRACTIONr_mcbond_other2.0483.49611023
X-RAY DIFFRACTIONr_mcangle_it3.1185.23713780
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B430920.04
12A430920.04
21B421480.05
22C421480.05
31B420760.05
32D420760.05
41A421620.05
42C421620.05
51A421850.05
52D421850.05
61C418220.05
62D418220.05
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 860 -
Rwork0.324 16411 -
all-17271 -
obs--99.06 %

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