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

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Basic information

Entry
Database: PDB / ID: 4gvh
TitleCrystal structure of Salmonella typhimurium family 3 glycoside hydrolase (NagZ) covalently bound to 5-fluoro-GlcNAc.
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE/SUBSTRATE / TIM-BARREL / HYDROLASE / 5-F-GlcNAc / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / 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 ...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
5-fluoro-N-acetyl-alpha-D-glucosamine / Beta-hexosaminidase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,1225
Polymers77,4482
Non-polymers6743
Water15,205844
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1583
Polymers38,7241
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9632
Polymers38,7241
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.260, 65.923, 94.724
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-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-0XY / 5-fluoro-N-acetyl-alpha-D-glucosamine / N-[(2S,3R,4R,5S,6S)-6-fluoro-2,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-3-yl]acetamide


Type: D-saccharide, alpha linking / Mass: 239.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14FNO6
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 296 K / pH: 6.5
Details: 0.1 M 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: 1.45→48.62 Å / Num. obs: 105508 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 11.19 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.428 / % possible all: 96.7

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Processing

Software
NameVersionClassification
MxDCdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→48.62 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 3154 2.99 %
Rwork0.165 --
obs0.166 105452 99.5 %
all-105508 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.83 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6967 Å20 Å20.3243 Å2
2--3.6598 Å20 Å2
3----2.9631 Å2
Refinement stepCycle: LAST / Resolution: 1.45→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 42 844 5995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065331
X-RAY DIFFRACTIONf_angle_d1.0787231
X-RAY DIFFRACTIONf_dihedral_angle_d17.1522008
X-RAY DIFFRACTIONf_chiral_restr0.071792
X-RAY DIFFRACTIONf_plane_restr0.006956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47160.32771330.27214035X-RAY DIFFRACTION91
1.4716-1.49460.25151250.24494384X-RAY DIFFRACTION98
1.4946-1.51910.27211260.21894417X-RAY DIFFRACTION100
1.5191-1.54530.22081360.20564429X-RAY DIFFRACTION100
1.5453-1.57340.24931500.19014437X-RAY DIFFRACTION100
1.5734-1.60370.19431270.17614515X-RAY DIFFRACTION100
1.6037-1.63640.20631350.1684442X-RAY DIFFRACTION100
1.6364-1.6720.21021470.17134420X-RAY DIFFRACTION100
1.672-1.71090.20361440.16454451X-RAY DIFFRACTION100
1.7109-1.75370.19851350.15684493X-RAY DIFFRACTION100
1.7537-1.80110.20741370.15864427X-RAY DIFFRACTION100
1.8011-1.85410.19711370.15624461X-RAY DIFFRACTION100
1.8541-1.9140.18341390.16094460X-RAY DIFFRACTION100
1.914-1.98240.21591370.1634454X-RAY DIFFRACTION100
1.9824-2.06180.1771380.15884486X-RAY DIFFRACTION100
2.0618-2.15560.16891370.16414463X-RAY DIFFRACTION100
2.1556-2.26930.20161390.15964470X-RAY DIFFRACTION100
2.2693-2.41140.17211360.15674457X-RAY DIFFRACTION100
2.4114-2.59760.20751380.15874495X-RAY DIFFRACTION100
2.5976-2.8590.19051380.15994481X-RAY DIFFRACTION100
2.859-3.27260.18631390.15654513X-RAY DIFFRACTION100
3.2726-4.12280.15641400.1434537X-RAY DIFFRACTION100
4.1228-48.64330.19251410.16784571X-RAY DIFFRACTION100

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