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

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Basic information

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


beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / beta-N-acetylglucosaminidase activity / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / response to antibiotic / cytosol
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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)77,8384
Polymers77,4482
Non-polymers3902
Water12,520695
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9192
Polymers38,7241
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9192
Polymers38,7241
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.620, 66.280, 95.220
Angle α, β, γ (deg.)90.00, 99.46, 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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 38.32 %
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: 0.97949
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→38.32 Å / Num. obs: 67010 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.27 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.123 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TR9

1tr9


Resolution: 1.7→38.32 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1999 2.99 %
Rwork0.167 --
obs0.169 66965 99.8 %
all-67010 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.88 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5912 Å20 Å20.0274 Å2
2--4.1454 Å20 Å2
3----1.5543 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 24 695 5825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065248
X-RAY DIFFRACTIONf_angle_d1.0227089
X-RAY DIFFRACTIONf_dihedral_angle_d13.1591957
X-RAY DIFFRACTIONf_chiral_restr0.068765
X-RAY DIFFRACTIONf_plane_restr0.004936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76080.27371990.21696485X-RAY DIFFRACTION100
1.7608-1.83130.24431990.20176451X-RAY DIFFRACTION100
1.8313-1.91460.2331990.18016478X-RAY DIFFRACTION100
1.9146-2.01560.2161990.16876448X-RAY DIFFRACTION100
2.0156-2.14180.20882000.1576499X-RAY DIFFRACTION100
2.1418-2.30720.18881990.15826493X-RAY DIFFRACTION100
2.3072-2.53930.20192010.16366502X-RAY DIFFRACTION100
2.5393-2.90670.21742000.16456513X-RAY DIFFRACTION100
2.9067-3.66160.19542010.16186524X-RAY DIFFRACTION100
3.6616-38.32840.18812020.16086573X-RAY DIFFRACTION99

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