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- PDB-5a56: The structure of GH101 from Streptococcus pneumoniae TIGR4 in com... -

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Basic information

Entry
Database: PDB / ID: 5a56
TitleThe structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with 1-O-methyl-T-antigen
ComponentsENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / ENDO-BETA-N-ACETYLGALACTOSAMINIDASE / GLYCOSIDE HYDROLASE FAMILY 101 / GH101 / T-ANTIGEN / MUCIN DEGRADATION
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase / mucinaminylserine mucinaminidase activity / glycopeptide alpha-N-acetylgalactosaminidase activity / metabolic process / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / : / Endo-alpha-N-acetylgalactosaminidase, helical bundle domain / Endo-alpha-N-acetylgalactosaminidase, domain 5 / Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain ...: / : / Endo-alpha-N-acetylgalactosaminidase, helical bundle domain / Endo-alpha-N-acetylgalactosaminidase, domain 5 / Glycosyl hydrolase 101, beta-sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase, N-terminal / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Glycosyl hydrolase 101 beta sandwich domain / Galactose-binding domain-like / Endo-alpha-N-acetylgalactosaminidase N-terminal domain / Galactose mutarotase-like fold domain / Endo-alpha-N-acetylgalactosaminidase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / YSIRK type signal peptide / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / YSIRK Gram-positive signal peptide / Beta-galactosidase; Chain A, domain 5 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / Endo-alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGregg, K.J. / Suits, M.D.L. / Deng, L. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism.
Authors: Gregg, K.J. / Suits, M.D. / Deng, L. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionJun 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_status / reflns / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_special_symmetry / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.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: ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,53939
Polymers125,6581
Non-polymers2,88138
Water27,6711536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.713, 121.764, 139.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-3761-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE


Mass: 125657.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 317-1425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2MGH6, endo-alpha-N-acetylgalactosaminidase
#2: Polysaccharide beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAc[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_1*OC_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1573 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1536 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 129705 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.185 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17841 6867 5 %RANDOM
Rwork0.15207 ---
obs0.1534 129705 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8755 0 181 1536 10472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199351
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.93512664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7951169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67425466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.526151544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541539
X-RAY DIFFRACTIONr_chiral_restr0.1460.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027166
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_it0.8541.5274494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3042.2845633
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7071.714857
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 478 -
Rwork0.221 9485 -
obs--99.22 %

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