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- PDB-5g2m: Crystal structure of NagZ from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5g2m
TitleCrystal structure of NagZ from Pseudomonas aeruginosa in complex with N-acetylglucosamine
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / BETA-HEXOSAMINIDASE / PEPTIDOGLYCAN
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 speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 9, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)77,0784
Polymers76,6352
Non-polymers4422
Water00
1
A: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5392
Polymers38,3181
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5392
Polymers38,3181
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.317, 74.550, 76.032
Angle α, β, γ (deg.)90.00, 110.28, 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 / NAGZ


Mass: 38317.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BOTH PROTEIN CHAINS CONTAIN A HIS RESIDUE AT POSITION -1 FROM THE FUSION TAG USED FOR PURIFICATION
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / 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
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): NAG COMES FROM THE HYDROLYSIS OF THE SUBSTRATE NAG-ANHYDROMUR ...N-ACETYL-D-GLUCOSAMINE (NAG): NAG COMES FROM THE HYDROLYSIS OF THE SUBSTRATE NAG-ANHYDROMUR PENTAPEPTIDE THAT WAS USED FOR THE SOAKING
Sequence detailsTHE SEQUENCE CONTAINS A HIS-TAG AT THE N-TERMINUS CONTAINING A THROMBIN CLEAVAGE SITE

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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: 2.04 Å3/Da / Density % sol: 39.6 % / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.87292
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2015 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87292 Å / Relative weight: 1
ReflectionResolution: 3→47.33 Å / Num. obs: 13847 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Biso Wilson estimate: 67.94 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / % 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: 3→45.441 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 29.19 / Stereochemistry target values: ML
Details: RESIDUES 171-173 FROM CHAIN A AND RESIDUES 170-173 FROM CHAIN B ARE NOT IN THE STRUCTURE SINCE THERE ARE NO ELECTRON DENSITY TO FIGURE OUT WHERE THEY REALLY ARE
RfactorNum. reflection% reflection
Rfree0.2653 672 4.9 %
Rwork0.2117 --
obs0.2142 13822 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.37 Å2
Refinement stepCycle: LAST / Resolution: 3→45.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 30 0 5075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025173
X-RAY DIFFRACTIONf_angle_d0.5657006
X-RAY DIFFRACTIONf_dihedral_angle_d17.4143126
X-RAY DIFFRACTIONf_chiral_restr0.039773
X-RAY DIFFRACTIONf_plane_restr0.004936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23160.38521400.34382586X-RAY DIFFRACTION100
3.2316-3.55670.39021330.27532614X-RAY DIFFRACTION99
3.5567-4.07110.27451390.22712625X-RAY DIFFRACTION100
4.0711-5.1280.22831270.18042634X-RAY DIFFRACTION100
5.128-45.44630.21061330.16742691X-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)
12.42080.65911.54182.10880.15894.53790.1913-0.0335-0.37270.0767-0.1233-0.00480.5598-0.4927-0.04780.5815-0.08950.09140.4534-0.04690.464969.2809-10.7582165.2091
28.1641.53936.58976.3536-3.43718.9488-0.08850.947-1.1187-1.05230.0498-0.12990.165-0.18370.11090.8352-0.1805-0.1010.6665-0.12270.596467.7081-5.2827154.8374
32.98560.7150.43947.3327-3.0738.90210.0672-0.2732-0.08440.20550.25790.2413-0.3689-0.4016-0.28910.4093-0.04860.04960.5113-0.15570.47673.173-3.8129168.5181
47.17441.1372-0.7974.43491.5438.9575-0.21840.10430.3545-0.0546-0.13330.63150.2275-0.26030.32890.5031-0.05140.00550.31540.03340.414480.0404-46.8851167.5791
55.57231.3258-2.14343.85280.57482.16310.15940.03840.9655-0.2710.23220.3821-1.21990.7705-0.27550.9443-0.2558-0.0590.7108-0.01560.694692.337-29.254172.9267
62.49780.7257-1.18013.8537-0.19853.9469-0.20550.48850.3394-0.79440.3311-0.3172-0.49291.0269-0.01690.6676-0.3391-0.04870.75810.0330.6771101.5446-34.0361158.7539
72.5699-0.1496-0.50834.67350.05243.5504-0.15050.5404-0.0647-1.0540.4902-0.331-0.03250.0114-0.23820.7956-0.14520.05360.68020.10210.504689.7449-46.6267153.7598
82.86590.2247-1.00563.4243.30487.32610.0235-0.97610.0650.89670.1854-0.06250.39810.8292-0.27120.6349-0.025-0.01150.76050.03360.565391.1734-38.8032179.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 232 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 233 THROUGH 256 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 257 THROUGH 332 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID -1 THROUGH 66 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 67 THROUGH 126 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 127 THROUGH 232 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 233 THROUGH 291 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 292 THROUGH 332 )

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