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- PDB-5a6j: GH20C, Beta-hexosaminidase from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 5a6j
TitleGH20C, Beta-hexosaminidase from Streptococcus pneumoniae
ComponentsN-ACETYL-BETA-D-GLUCOSAMINIDASE
KeywordsHYDROLASE / BETA-HEXOSAMINIDASE / STREPTOCOCCUS PNEUMONIAE / BACTERIAL PROTEINS / CARBOHYDRATE CONFORMATION / CATALYTIC DOMAIN / HOST-PATHOGEN INTERACTIONS / HYDROGEN BONDING / HYDROLYSIS / MODELS / POLYSACCHARIDES / 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
Glycosyl hydrolase-related protein / N-acetyl-beta-D-glucosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 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 1.1Mar 22, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Jan 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. SHEET DETERMINATION METHOD: DSSP 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" 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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" 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
B: N-ACETYL-BETA-D-GLUCOSAMINIDASE
C: N-ACETYL-BETA-D-GLUCOSAMINIDASE
D: N-ACETYL-BETA-D-GLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,7885
Polymers296,7264
Non-polymers621
Water29,1661619
1
A: N-ACETYL-BETA-D-GLUCOSAMINIDASE
C: N-ACETYL-BETA-D-GLUCOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)148,3632
Polymers148,3632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-32.7 kcal/mol
Surface area42040 Å2
MethodPISA
2
B: N-ACETYL-BETA-D-GLUCOSAMINIDASE
hetero molecules

D: N-ACETYL-BETA-D-GLUCOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)148,4253
Polymers148,3632
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area6690 Å2
ΔGint-27.8 kcal/mol
Surface area41470 Å2
MethodPISA
3
D: N-ACETYL-BETA-D-GLUCOSAMINIDASE

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


Theoretical massNumber of molelcules
Total (without water)148,4253
Polymers148,3632
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area6690 Å2
ΔGint-27.8 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.840, 136.940, 202.350
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
N-ACETYL-BETA-D-GLUCOSAMINIDASE / GH20C


Mass: 74181.516 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / 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: 2.22 Å3/Da / Density % sol: 44.65 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV++ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→50.7 Å / Num. obs: 184285 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.9 / % possible all: 96.9

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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: 1.94→113.41 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.66 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 9269 5 %RANDOM
Rwork0.20591 ---
obs0.20853 174931 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---1.32 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.94→113.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19496 0 4 1619 21119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01919968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218630
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.94427107
X-RAY DIFFRACTIONr_angle_other_deg0.792342676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22852461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94724.668994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.988153333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9461599
X-RAY DIFFRACTIONr_chiral_restr0.0750.23018
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024779
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_it0.9771.9749829
X-RAY DIFFRACTIONr_mcbond_other0.9771.9749828
X-RAY DIFFRACTIONr_mcangle_it1.5942.95612274
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0222.02210139
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: 1.944→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 664 -
Rwork0.332 12818 -
obs--96.87 %

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