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- PDB-5g5k: Crystal structure of NagZ from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 5g5k
TitleCrystal structure of NagZ from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / N-ACETYLGLUCOSAMINIDASE / BETA-HEXOSAMINIDASE / INHIBITION / 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
2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN / Beta-hexosaminidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionMay 25, 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 1.3Sep 20, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_wavelength_list
Revision 1.4May 1, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: BETA-HEXOSAMINIDASE
B: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0444
Polymers76,6352
Non-polymers4082
Water1267
1
A: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5222
Polymers38,3181
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5222
Polymers38,3181
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.224, 67.607, 74.064
Angle α, β, γ (deg.)90.00, 97.83, 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: Chemical ChemComp-NOK / 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN


Mass: 204.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-ACETAMIDO-1,2-DIDEOXYNOJIRIMYCIN (IMI): THIS COMPOUND ACTS AS AN INHIBITOR OF NAGZ FROM ...2-ACETAMIDO-1,2-DIDEOXYNOJIRIMYCIN (IMI): THIS COMPOUND ACTS AS AN INHIBITOR OF NAGZ FROM PSEUDOMONAS AERUGINOSA
Sequence detailsBOTH PROTEIN CHAINS CONTAIN A HIS RESIDUE AT POSITION -1 FROM THE FUSION TAG USED FOR PURIFICATION

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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: 2.11 Å3/Da / Density % sol: 41.85 % / 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: SLS / Beamline: X06DA / Wavelength: 0.97945 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2015 / Details: TOROIDAL MIRROR
RadiationMonochromator: DUAL CHANNEL CUT CRYSTALS (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.1→41.28 Å / Num. obs: 11501 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 72.51 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.7
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / % 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: 3.1→41.289 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 338 3 %
Rwork0.2387 --
obs0.2401 11475 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.04 Å2
Refinement stepCycle: LAST / Resolution: 3.1→41.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 28 7 5117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035209
X-RAY DIFFRACTIONf_angle_d0.5197057
X-RAY DIFFRACTIONf_dihedral_angle_d20.1333143
X-RAY DIFFRACTIONf_chiral_restr0.038777
X-RAY DIFFRACTIONf_plane_restr0.004946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.90550.33121560.2715618X-RAY DIFFRACTION99
3.9055-41.29280.26441820.22275519X-RAY DIFFRACTION96
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)
15.5221-1.45932.16234.0881-3.8998.4835-0.1264-0.6715-0.50130.17850.2829-0.53250.6723-0.5681-0.15440.5753-0.05280.0130.5359-0.08950.259819.7616-5.3261-7.441
21.9563-0.05590.78742.5674-2.1073.1859-0.07680.0176-0.0148-0.22170.26770.27970.07840.2270.09380.66960.08010.11390.31140.16710.236728.1247-2.8646-3.187
35.7177-1.5391-3.50194.06170.33162.23830.077-0.67020.16370.05340.00540.2447-0.34240.2758-0.07750.74130.05780.05370.464-0.06690.301925.113311.228411.8459
46.6574-0.72580.93852.4275-0.79962.4104-0.016-0.0673-0.49970.420.00820.53730.2266-0.79180.14830.7489-0.13040.02680.5446-0.13530.32868.690712.30097.6834
53.0191-0.1156-0.41079.19692.60485.8958-0.2511-0.02940.82670.45880.46860.43080.1029-0.2612-0.1180.643-0.04670.14620.2969-0.18020.607314.326122.92284.859
67.746-1.8479-0.66164.74792.20884.2998-0.08-0.0672-0.19840.2051-0.11020.50320.1113-0.29730.17490.52710.12810.10810.19930.02040.27977.042414.5061-2.3737
77.66090.38140.01492.8034-0.84935.68380.2812-0.38810.2549-0.3146-0.14930.34590.4986-0.3885-0.11040.56390.0687-0.0370.3437-0.12330.327910.63913.0566-11.6085
87.843-0.27077.09520.9072-0.16617.71560.62521.04020.72760.2102-0.6462-0.24240.9942.0373-0.08441.0872-0.03230.12580.69490.11190.599337.3677.4317.9138
91.391-0.0669-0.61462.48540.15534.10520.37010.12230.2027-0.0028-0.06830.3057-0.88610.3692-0.09410.68180.15250.06290.1947-0.07240.392813.515-0.652940.1795
101.8-0.1081-1.07290.7290.05921.84310.055-0.0750.0123-0.16230.0235-0.0375-0.12450.334-0.12480.65310.01660.2390.3705-0.17880.176922.3452-3.49938.5972
112.2657-1.40330.31025.37463.78744.09980.0117-0.1807-0.1889-0.0978-0.05170.3923-0.3537-0.0866-0.11140.6791-0.13770.13060.62290.0080.195126.1002-11.33519.5083
124.28220.89590.71510.21140.37281.87460.030.2306-0.7805-0.48820.0667-0.1981-0.3822-0.1894-0.0530.48320.16030.16840.2879-0.08870.366322.3958-17.034423.6845
138.0073-1.28840.76622.4681-0.07440.47280.08510.222-0.4192-0.16180.13530.27890.0166-0.2224-0.28890.7042-0.02890.10430.35760.03370.259711.4241-23.540824.7995
146.9191-1.67732.09413.46661.57223.8268-0.6032-0.9998-0.0949-0.19220.4064-0.02390.2092-0.07960.09270.5379-0.00120.14670.44130.06720.28393.4748-17.688834.6708
153.80042.33262.11725.362-0.66372.16470.2437-0.74220.36170.3986-0.39310.83580.1446-0.1975-0.72250.92040.2120.22210.6370.03710.3055.6959-9.905845.4614
164.7642.4825-4.17421.5599-2.16219.61760.5558-0.59060.1150.7321-0.0561-0.4575-0.66181.0076-0.08920.65080.12260.25530.3220.1260.565436.4875-12.975728.8624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 40 THROUGH 66 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 67 THROUGH 154 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 155 THROUGH 183 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 184 THROUGH 206 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 207 THROUGH 256 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 257 THROUGH 298 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 299 THROUGH 332 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 1 THROUGH 39 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 40 THROUGH 66 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 67 THROUGH 89 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 90 THROUGH 136 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 137 THROUGH 217 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 218 THROUGH 277 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 278 THROUGH 301 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 302 THROUGH 332 )

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