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- PDB-5a69: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in compl... -

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Basic information

Entry
Database: PDB / ID: 5a69
TitleGH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-PUGNAc
ComponentsN-ACETYL-BETA-D-GLUCOSAMINIDASE
KeywordsHYDROLASE / BETA-HEXOSAMINIDASE / CARBOHYDRATE CONFORMATION / CATALYTIC DOMAIN / ENZYME INHIBITORS / HOST-PATHOGEN INTERACTIONS / HYDROGEN BONDING / HYDROLYSIS / POLYSACCHARIDES / PROTEIN BINDING / VIRULENCE FACTORS
Function / homology
Function and homology information


hexosaminidase activity / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function
N-acetyl-beta-d-glucosaminidase / Glycoside Hydrolase 20C, C-terminal / N-acetyl-beta-D-glucosaminidase, N-terminal / Glycoside Hydrolase 20C C-terminal domain / N-acetyl-beta-D-glucosaminidase N-terminal domain / Hexosaminidase D-like / N-acetyl-b-d-glucoasminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Double Stranded RNA Binding Domain ...N-acetyl-beta-d-glucosaminidase / Glycoside Hydrolase 20C, C-terminal / N-acetyl-beta-D-glucosaminidase, N-terminal / Glycoside Hydrolase 20C C-terminal domain / N-acetyl-beta-D-glucosaminidase N-terminal domain / Hexosaminidase D-like / N-acetyl-b-d-glucoasminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Double Stranded RNA Binding Domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-OGN / Glycosyl hydrolase-related protein / N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCid, M. / Robb, C.S. / Higgins, M.A. / Boraston, A.B.
CitationJournal: J. Biol. Chem. / Year: 2015
Title: A Second beta-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans.
Authors: Robb, M. / Robb, C.S. / Higgins, M.A. / Hobbs, J.K. / Paton, J.C. / Boraston, A.B.
History
DepositionJun 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYL-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5352
Polymers74,1821
Non-polymers3531
Water70339
1
A: N-ACETYL-BETA-D-GLUCOSAMINIDASE
hetero molecules

A: N-ACETYL-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0704
Polymers148,3632
Non-polymers7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6060 Å2
ΔGint-32.5 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.780, 95.580, 131.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein N-ACETYL-BETA-D-GLUCOSAMINIDASE / GH20C


Mass: 74181.516 Da / Num. of mol.: 1
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: C1CH75, UniProt: A0A0H2US73*PLUS
#2: Chemical ChemComp-OGN / [(Z)-[(3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-ylidene]amino] N-phenylcarbamate / Gal-PUGNAc


Mass: 353.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N3O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.86 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 10.2
Details: 12% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1%GLYCEROL

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.12709
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. obs: 27418 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EPN

2epn


Resolution: 2.2→19.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.902 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28592 1381 5.1 %RANDOM
Rwork0.23217 ---
obs0.23498 25951 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.143 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--3.59 Å20 Å2
3----4.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 25 39 4451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194501
X-RAY DIFFRACTIONr_bond_other_d0.0010.024013
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9446122
X-RAY DIFFRACTIONr_angle_other_deg0.85539115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38824.08201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7251523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 91 -
Rwork0.279 1901 -
obs--97.98 %

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