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

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Basic information

Entry
Database: PDB / ID: 4hzm
TitleCrystal structure of Salmonella typhimurium family 3 glycoside hydrolase (NagZ) bound to N-[(3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]butanamide
ComponentsBeta-hexosaminidaseHexosaminidase
Keywordshydrolase/hydrolase inhibitor / TIM-BARREL / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division ...peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / 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
Chem-1BW / 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: Chembiochem / Year: 2013
Title: The Development of Selective Inhibitors of NagZ: Increased Susceptibility of Gram-Negative Bacteria to beta-Lactams.
Authors: Stubbs, K.A. / Bacik, J.P. / Perley-Robertson, G.E. / Whitworth, G.E. / Gloster, T.M. / Vocadlo, D.J. / Mark, B.L.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Sep 20, 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)78,1085
Polymers77,4482
Non-polymers6603
Water16,574920
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9562
Polymers38,7241
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1513
Polymers38,7241
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.765, 66.187, 95.065
Angle α, β, γ (deg.)90.00, 99.21, 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-1BW / N-[(3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]butanamide


Type: D-saccharide / Mass: 232.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20N2O4
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 920 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / 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 Å
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→49.12 Å / Num. all: 105765 / Num. obs: 105765 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.077 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.077 / Net I/σ(I): 13
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.1 / Num. unique all: 13664 / Rsym value: 0.468 / % possible all: 87.5

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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
Starting model: PDB ENTRY 4GVG

4gvg


Resolution: 1.45→49.12 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 3160 2.99 %RANDOM
Rwork0.1693 ---
obs0.17 105697 97.96 %-
all-105765 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.409 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4426 Å20 Å2-0.6958 Å2
2--4.4633 Å20 Å2
3----1.0207 Å2
Refinement stepCycle: LAST / Resolution: 1.45→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 44 920 6026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085291
X-RAY DIFFRACTIONf_angle_d1.1727168
X-RAY DIFFRACTIONf_dihedral_angle_d12.5061964
X-RAY DIFFRACTIONf_chiral_restr0.067785
X-RAY DIFFRACTIONf_plane_restr0.007946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47170.28031150.25833642X-RAY DIFFRACTION80
1.4717-1.49460.29681190.24753895X-RAY DIFFRACTION87
1.4946-1.51920.21621120.24654183X-RAY DIFFRACTION92
1.5192-1.54540.2491390.2234307X-RAY DIFFRACTION95
1.5454-1.57350.24221450.20254499X-RAY DIFFRACTION99
1.5735-1.60370.2321300.18834525X-RAY DIFFRACTION100
1.6037-1.63650.22621460.17354522X-RAY DIFFRACTION100
1.6365-1.6720.19061460.17974516X-RAY DIFFRACTION100
1.672-1.71090.21031450.17214541X-RAY DIFFRACTION100
1.7109-1.75370.21071350.1694527X-RAY DIFFRACTION100
1.7537-1.80110.18361410.16684564X-RAY DIFFRACTION100
1.8011-1.85410.23161410.16344534X-RAY DIFFRACTION100
1.8541-1.9140.1751390.16394539X-RAY DIFFRACTION100
1.914-1.98240.19841390.17024539X-RAY DIFFRACTION100
1.9824-2.06180.1721400.16754575X-RAY DIFFRACTION100
2.0618-2.15560.19111370.17154534X-RAY DIFFRACTION100
2.1556-2.26930.19611450.16584555X-RAY DIFFRACTION100
2.2693-2.41140.16981380.16024523X-RAY DIFFRACTION100
2.4114-2.59760.18331420.15784581X-RAY DIFFRACTION100
2.5976-2.8590.19481400.16394589X-RAY DIFFRACTION100
2.859-3.27260.19061380.16164560X-RAY DIFFRACTION100
3.2726-4.12280.1631450.14254627X-RAY DIFFRACTION100
4.1228-49.15110.1781430.16444660X-RAY DIFFRACTION100

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