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- PDB-4gvf: Crystal structure of Salmonella typhimurium family 3 glycoside hy... -

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Basic information

Entry
Database: PDB / ID: 4gvf
TitleCrystal structure of Salmonella typhimurium family 3 glycoside hydrolase (NagZ) bound to GlcNAc
ComponentsBeta-hexosaminidaseHexosaminidase
KeywordsHYDROLASE / TIM-BARREL
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / response to antibiotic / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Beta-hexosaminidase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBacik, J.P. / Mark, B.L.
CitationJournal: Chem.Biol. / Year: 2012
Title: Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion.
Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Vocadlo, D.J. / Mark, B.L.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Atomic model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-hexosaminidase
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5287
Polymers77,4482
Non-polymers1,0805
Water17,799988
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1663
Polymers38,7241
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3624
Polymers38,7241
Non-polymers6383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.544, 66.233, 94.968
Angle α, β, γ (deg.)90.00, 99.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-hexosaminidase / Hexosaminidase / Beta-N-acetylhexosaminidase / N-acetyl-beta-glucosaminidase


Mass: 38723.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: nagZ, STM1209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZQ06, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 296 K / pH: 6.5
Details: 0.1M MES, 25% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→48.89 Å / Num. obs: 131665 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 9.14 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.07 / Net I/σ(I): 13.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.29 / % possible all: 93.7

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Processing

Software
NameVersionClassification
MxDCdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.89 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 3884 3.02 %
Rwork0.167 --
obs0.168 128758 96.9 %
all-131665 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.63 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7979 Å20 Å2-0.0108 Å2
2--4.7913 Å20 Å2
3----1.9935 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 72 988 6189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055366
X-RAY DIFFRACTIONf_angle_d1.0667279
X-RAY DIFFRACTIONf_dihedral_angle_d16.5552043
X-RAY DIFFRACTIONf_chiral_restr0.067794
X-RAY DIFFRACTIONf_plane_restr0.005965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.39830.22173430.218110845X-RAY DIFFRACTION85
1.3983-1.45420.22953830.197412103X-RAY DIFFRACTION94
1.4542-1.52040.19033840.176112372X-RAY DIFFRACTION96
1.5204-1.60060.19763920.160212549X-RAY DIFFRACTION98
1.6006-1.70090.17754000.159312648X-RAY DIFFRACTION98
1.7009-1.83220.19513960.160612718X-RAY DIFFRACTION99
1.8322-2.01660.18183910.165312761X-RAY DIFFRACTION99
2.0166-2.30840.17463940.161412868X-RAY DIFFRACTION100
2.3084-2.90830.20143990.168712921X-RAY DIFFRACTION100
2.9083-48.92280.18094020.159613089X-RAY DIFFRACTION100

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