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- PDB-4azg: Differential inhibition of the tandem GH20 catalytic modules in t... -

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Basic information

Entry
Database: PDB / ID: 4azg
TitleDifferential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, StrH
ComponentsBETA-N-ACETYLHEXOSAMINIDASEHexosaminidase
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
AF1782-like / G5 domain / G5 domain / G5 domain profile. / G5 / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / YSIRK type signal peptide / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / YSIRK Gram-positive signal peptide ...AF1782-like / G5 domain / G5 domain / G5 domain profile. / G5 / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / YSIRK type signal peptide / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-OAN / Beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPluvinage, B. / Stubbs, K.A. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: Org.Biomol.Chem. / Year: 2013
Title: Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N-Acetylglucosaminidase, Strh.
Authors: Pluvinage, B. / Stubbs, K.A. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionJun 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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_sheet / 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_sheet.number_strands / _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 "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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: BETA-N-ACETYLHEXOSAMINIDASE
B: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,20119
Polymers99,5822
Non-polymers1,62017
Water9,836546
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A: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,63210
Polymers49,7911
Non-polymers8419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-N-ACETYLHEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5709
Polymers49,7911
Non-polymers7798
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.700, 115.200, 129.900
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 BETA-N-ACETYLHEXOSAMINIDASE / Hexosaminidase / GLYCOSIDE HYDROLASE 20


Mass: 49790.934 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 627-1064
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49610, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-OAN / O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE / PUGNAc / PUGNAc


Mass: 353.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N3O7 / Comment: inhibitor*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.51 Å3/Da / Density % sol: 50.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 39589 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.4 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YL5

2yl5


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.683 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24751 1989 5 %RANDOM
Rwork0.19044 ---
obs0.19334 37539 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 110 546 7187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026929
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9619361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19625.303330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5621519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215339
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_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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 126 -
Rwork0.218 2501 -
obs--96.65 %

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