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- PDB-5a6k: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in compl... -

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Basic information

Entry
Database: PDB / ID: 5a6k
TitleGH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT
ComponentsGH20C
KeywordsHYDROLASE / BETA-HEXOSAMINIDASE / STREPTOCOCCUS PNEUMONIAE / BACTERIAL PROTEINS / CARBOHYDRATE CONFORMATION / CATALYTIC DOMAIN / ENZYME INHIBITORS / HOST-PATHOGEN INTERACTIONS / HYDROGEN BONDING / HYDROLYSIS / MODELS / POLYSACCHARIDES / PROTEIN BINDING / VIRULENCE FACTORS
Function / homology
Function and homology information


hexosaminidase activity / beta-N-acetylhexosaminidase 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-NSG / Glycosyl hydrolase-related protein / N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: 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. THE SHEETS PRESENTED AS "BB" 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: GH20C
B: GH20C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,8064
Polymers148,3632
Non-polymers4432
Water19,7441096
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-34.1 kcal/mol
Surface area41010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.690, 99.420, 133.170
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 GH20C


Mass: 74181.516 Da / Num. of mol.: 2
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, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-NSG / (2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 221.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 2.2 Å3/Da / Density % sol: 44.11 % / 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97965
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.1→95.69 Å / Num. obs: 69114 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EPN

2epn


Resolution: 2.1→79.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.813 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22393 3339 4.8 %RANDOM
Rwork0.17255 ---
obs0.17501 65678 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.154 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---2.13 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→79.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9970 0 28 1096 11094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910228
X-RAY DIFFRACTIONr_bond_other_d0.0010.029587
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.94913884
X-RAY DIFFRACTIONr_angle_other_deg0.8143.00221966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23424.638511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.346151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.111553
X-RAY DIFFRACTIONr_chiral_restr0.0820.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022440
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_it0.7011.3575004
X-RAY DIFFRACTIONr_mcbond_other0.7011.3575003
X-RAY DIFFRACTIONr_mcangle_it1.1822.0336252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9651.4145224
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: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 217 -
Rwork0.18 4329 -
obs--83.23 %

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