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- PDB-2ygm: THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, T... -

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Basic information

Entry
Database: PDB / ID: 2ygm
TitleTHE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH98, THE FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAE SP3-BS71, IN COMPLEX WITH THE BLOOD GROUP B ANTIGEN
ComponentsBLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
KeywordsHYDROLASE / CARBOHYDRATE-BINDING MODULE / BLOOD GROUP ANTIGEN
Function / homology
Function and homology information


carbohydrate metabolic process / metal ion binding
Similarity search - Function
NPCBM/NEW2 domain / Glycosyl hydrolase family 98, C-terminal / Glycosyl hydrolase family 98, central domain / Glycosyl hydrolase family 98 / Glycosyl hydrolase family 98 C-terminal domain / Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Polysaccharide lyase family 8-like, C-terminal ...NPCBM/NEW2 domain / Glycosyl hydrolase family 98, C-terminal / Glycosyl hydrolase family 98, central domain / Glycosyl hydrolase family 98 / Glycosyl hydrolase family 98 C-terminal domain / Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Polysaccharide lyase family 8-like, C-terminal / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Blood group B H type 2 antigen, beta anomer / Blood group A-and B-cleaving endo-beta-galactosidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHiggins, M.A. / Ficko-Blean, E. / Wright, C. / Meloncelli, P.J. / Lowary, T.L. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Overall Architecture and Receptor Binding of Pneumococcal Carbohydrate Antigen Hydrolyzing Enzymes.
Authors: Higgins, M.A. / Ficko-Blean, E. / Wright, C. / Meloncelli, P.J. / Lowary, T.L. / Boraston, A.B.
History
DepositionApr 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 17, 2021Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_molecule_features / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_molecule
Item: _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
A: BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
B: BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7018
Polymers77,1912
Non-polymers1,5096
Water3,153175
1
A: BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3504
Polymers38,5961
Non-polymers7553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3504
Polymers38,5961
Non-polymers7553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 78.500, 131.580
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 BLOOD GROUP A-AND B-CLEAVING ENDO-BETA-GALACTOSIDASE


Mass: 38595.664 Da / Num. of mol.: 2 / Fragment: CBM51-1.2, RESIDUES 66-413
Source method: isolated from a genetically manipulated source
Details: TANDEM FAMILY 51 CBMS / Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP3-BS71 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1CB04
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido- ...alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 691.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group B H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3-4/a4-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.45 Å3/Da / Density % sol: 49.42 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9214
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9214 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 31713 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNR

2vnr


Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.918 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29728 1691 5.1 %RANDOM
Rwork0.24521 ---
obs0.24783 31713 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.314 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å20 Å20 Å2
2--2.54 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 98 175 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.9657639
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04325.885243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56515955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7611510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021415
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_it0.3461.53480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63125634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53732151
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9324.52004
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 116 -
Rwork0.333 2301 -
obs--99.83 %

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