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- PDB-5g3r: Crystal structure of NagZ from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5g3r
TitleCrystal structure of NagZ from Pseudomonas aeruginosa in complex with N-acetylglucosamine and L-Ala-1,6-anhydroMurNAc
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / N-ACETYLGLUCOSAMINIDASE / BETA-HEXOSAMINIDASE / PEPTIDOGLYCAN
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
Chem-89A / DI(HYDROXYETHYL)ETHER / Beta-hexosaminidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsAcebron, I. / Artola-Recolons, C. / Mahasenan, K. / Mobashery, S. / Hermoso, J.A.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.
Authors: Acebron, I. / Mahasenan, K.V. / De Benedetti, S. / Lee, M. / Artola-Recolons, C. / Hesek, D. / Wang, H. / Hermoso, J.A. / Mobashery, S.
History
DepositionApr 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_initial_refinement_model / struct_ref / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

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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)77,9818
Polymers76,6352
Non-polymers1,3456
Water4,558253
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8843
Polymers38,3181
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0965
Polymers38,3181
Non-polymers7794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.657, 74.629, 75.560
Angle α, β, γ (deg.)90.00, 110.94, 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: 38317.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAIN A CONTAINS A SMALL FRAGMENT (GSH) FROM THE FUSION TAG USED FOR PURIFICATION, AND CHAIN B CONTAINS ONLY A HIS RESIDUE AT POSITION -1 FROM THE SAME FUSION TAG
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: nagZ, PA3005 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZK0, 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-89A / 2-[[(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoyl]amino]propanamide


Mass: 345.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23N3O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-ALA-1,6-ANHYDRO-N-ACETYLMURAMIC ACID (89A): THIS MOLECULES IS ONE OF THE PRODUCTS GENERATED BY ...L-ALA-1,6-ANHYDRO-N-ACETYLMURAMIC ACID (89A): THIS MOLECULES IS ONE OF THE PRODUCTS GENERATED BY THE HYDROLYSIS OF THE NAG-ANHYDROMUR PENTAPEPTIDE THAT WAS USED FOR THE SOAKING EXPERIMENTS N-ACETYL-D-GLUCOSAMINE (NAG): THIS MOLECULES IS ONE OF THE PRODUCTS GENERATED BY THE HYDROLYSIS OF THE NAG-ANHYDROMUR PENTAPEPTIDE THAT WAS USED FOR THE SOAKING EXPERIMENTS DI(HYDROXYETHYL)ETHER (PEG): PEG COMES FROM THE CRYSTALLIZATION CONDITIONS
Sequence detailsTHE SEQUENCE CONTAINS A HIS-TAG AT THE N-TERMINUS

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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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.18→47.8 Å / Num. obs: 36231 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 34.64 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA

Resolution: 2.18→47.804 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 27.86 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2417 1772 4.9 %
Rwork0.1942 --
obs0.1966 36197 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.07 Å2
Refinement stepCycle: LAST / Resolution: 2.18→47.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 92 253 5447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095294
X-RAY DIFFRACTIONf_angle_d1.0447171
X-RAY DIFFRACTIONf_dihedral_angle_d18.4343171
X-RAY DIFFRACTIONf_chiral_restr0.055795
X-RAY DIFFRACTIONf_plane_restr0.006956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.2390.34941410.27072642X-RAY DIFFRACTION100
2.239-2.30490.29911260.2562637X-RAY DIFFRACTION100
2.3049-2.37930.33931380.23972637X-RAY DIFFRACTION100
2.3793-2.46430.30461210.24182644X-RAY DIFFRACTION100
2.4643-2.5630.30721160.22732647X-RAY DIFFRACTION100
2.563-2.67960.30521440.22222644X-RAY DIFFRACTION100
2.6796-2.82080.29381370.21542608X-RAY DIFFRACTION100
2.8208-2.99760.26471210.21572666X-RAY DIFFRACTION100
2.9976-3.2290.26841400.22522659X-RAY DIFFRACTION100
3.229-3.55380.24961560.18332637X-RAY DIFFRACTION100
3.5538-4.06780.23121170.16642647X-RAY DIFFRACTION100
4.0678-5.12410.19011580.15522653X-RAY DIFFRACTION100
5.1241-47.81580.18061570.16852704X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.99771.2698-0.0272.6536-0.0642.21680.0167-0.0266-0.21620.1138-0.0696-0.1640.1752-0.13390.0370.26510.0154-0.00870.2272-0.01020.22338.3996-7.054168.3435
24.2780.56452.76284.68821.95742.3330.04620.5813-0.3395-0.4219-0.03710.17260.7405-0.32-0.13020.4101-0.10240.05030.2287-0.04810.18450.5036-11.42158.2755
33.45691.6611.17473.68690.86674.5822-0.16770.3839-0.0974-0.17890.03640.16680.406-0.47020.16160.2054-0.08-0.01010.357-0.05560.259-5.7147-9.0765152.035
41.6560.6676-0.64322.3639-1.35073.571-0.0242-0.0450.0265-0.0748-0.03880.0545-0.1323-0.10910.10720.21610.0102-0.00550.2321-0.0740.21375.615-1.1174163.2075
52.49031.1135-0.23112.27190.05612.183-0.0773-0.01760.26510.0083-0.01910.0363-0.18140.14730.06730.24640.0148-0.04360.21980.02320.212123.6148-34.1702168.2328
62.28292.2832-1.21694.16020.20224.6028-0.29380.32310.0302-0.66290.3158-0.2828-0.3450.49670.07420.2934-0.14770.01170.45610.01330.412137.1769-33.2626152.961
71.49971.01290.63213.3011.55053.709-0.0323-0.08330.0633-0.0926-0.0398-0.05990.0621-0.01180.12620.20510.0127-0.00690.2690.06110.25723.5328-40.0243164.1635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -3 THROUGH 153 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 154 THROUGH 173 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 174 THROUGH 227 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 228 THROUGH 332 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID -1 THROUGH 164 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 165 THROUGH 242 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 243 THROUGH 332 )

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