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- PDB-4gvi: Crystal structure of mutant (D248N) Salmonella typhimurium family... -

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Basic information

Entry
Database: PDB / ID: 4gvi
TitleCrystal structure of mutant (D248N) Salmonella typhimurium family 3 glycoside hydrolase (NagZ) in complex with GlcNAc-1,6-anhMurNAc
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / TIM-BARREL
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
Chem-AH0 / Beta-hexosaminidase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 18, 2013Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,6347
Polymers77,4462
Non-polymers1,1885
Water14,106783
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2193
Polymers38,7231
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4154
Polymers38,7231
Non-polymers6923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.670, 65.640, 94.910
Angle α, β, γ (deg.)90.00, 99.24, 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: 38722.949 Da / Num. of mol.: 2 / Fragment: unp residues 18-642 / Mutation: D248N
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-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


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
#3: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO7
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LINKED SUGAR COMPONENTS NAG AND AH0 REPRESENT GLCNAC-1,6-ANHMURNAC

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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→28.49 Å / Num. obs: 84880 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 17.89 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.192 / % possible all: 81.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→28.36 Å / SU ML: 0.53 / σ(F): 1.36 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 2553 3.01 %
Rwork0.171 --
obs0.172 84812 97 %
all-84880 -
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.09 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5693 Å2-0 Å20.9479 Å2
2--7.1338 Å2-0 Å2
3----2.5645 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 0 78 783 5938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085316
X-RAY DIFFRACTIONf_angle_d1.1827205
X-RAY DIFFRACTIONf_dihedral_angle_d12.5811982
X-RAY DIFFRACTIONf_chiral_restr0.07799
X-RAY DIFFRACTIONf_plane_restr0.006944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57980.27321060.24133202X-RAY DIFFRACTION69
1.5798-1.61210.23561180.20233932X-RAY DIFFRACTION83
1.6121-1.64710.20751410.18294527X-RAY DIFFRACTION97
1.6471-1.68540.22081620.17434637X-RAY DIFFRACTION99
1.6854-1.72760.23151390.16324673X-RAY DIFFRACTION100
1.7276-1.77430.19061470.16284700X-RAY DIFFRACTION100
1.7743-1.82650.21651380.16374676X-RAY DIFFRACTION100
1.8265-1.88540.18881480.1694651X-RAY DIFFRACTION100
1.8854-1.95280.21031460.17494711X-RAY DIFFRACTION100
1.9528-2.0310.19881460.17624680X-RAY DIFFRACTION100
2.031-2.12340.20731430.18274719X-RAY DIFFRACTION100
2.1234-2.23530.22361440.18354682X-RAY DIFFRACTION100
2.2353-2.37520.2031450.17544738X-RAY DIFFRACTION100
2.3752-2.55850.18921450.16734691X-RAY DIFFRACTION100
2.5585-2.81580.19791430.16584718X-RAY DIFFRACTION100
2.8158-3.22280.21151480.16674740X-RAY DIFFRACTION100
3.2228-4.05840.16781440.14634759X-RAY DIFFRACTION100
4.0584-28.35930.2071500.1834823X-RAY DIFFRACTION100

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