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- PDB-5g1m: Crystal structure of NagZ from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5g1m
TitleCrystal structure of NagZ from Pseudomonas aeruginosa
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / PEPTIDOGLYCAN / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / N-ACETYLGLUCOSAMINIDASE
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Beta-hexosaminidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)77,0017
Polymers76,6352
Non-polymers3665
Water10,269570
1
A: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5184
Polymers38,3181
Non-polymers2013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4833
Polymers38,3181
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.971, 75.289, 76.389
Angle α, β, γ (deg.)90.00, 110.10, 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 570 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE (CL): CHLORIDE ANION COMES FROM THE PROTEIN BUFFER SOLUTION ACETATE ION (ACT): ACETATE ...CHLORIDE (CL): CHLORIDE ANION COMES FROM THE PROTEIN BUFFER SOLUTION ACETATE ION (ACT): ACETATE IONS COME FROM THE CRYSTALLIZATION CONDITION DI(HYDROXYETHYL)ETHER (PEG): PEG MOLECULES COME FROM THE CRYSTALLIZATION CONDITION
Sequence detailsTHE PROTEIN SEQUENCE CONTAINS A HIS-TAG WITH A THROMBIN CLEAVAGE SITE AT THE N-TERMINUS WHOSE ...THE PROTEIN SEQUENCE CONTAINS A HIS-TAG WITH A THROMBIN CLEAVAGE SITE AT THE N-TERMINUS WHOSE SEQUENCE IS MGSSHHHHHHSSGLVPRGSH

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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: 2.26 Å3/Da / Density % sol: 45.55 % / 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: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→46.96 Å / Num. obs: 63078 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 5.8 % / Biso Wilson estimate: 15.32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OXN

2oxn


Resolution: 1.8→46.959 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 24.84 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2406 3180 5 %
Rwork0.1956 --
obs0.1979 63043 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 23 570 5685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085232
X-RAY DIFFRACTIONf_angle_d1.0647088
X-RAY DIFFRACTIONf_dihedral_angle_d17.8083174
X-RAY DIFFRACTIONf_chiral_restr0.054778
X-RAY DIFFRACTIONf_plane_restr0.006952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82690.34551450.30272608X-RAY DIFFRACTION100
1.8269-1.85540.32061360.27562574X-RAY DIFFRACTION100
1.8554-1.88580.30021410.26062600X-RAY DIFFRACTION100
1.8858-1.91840.32391430.23942584X-RAY DIFFRACTION100
1.9184-1.95320.29911390.24352588X-RAY DIFFRACTION100
1.9532-1.99080.29131350.2342583X-RAY DIFFRACTION100
1.9908-2.03150.29951450.222595X-RAY DIFFRACTION100
2.0315-2.07560.25251360.21542588X-RAY DIFFRACTION100
2.0756-2.12390.24771510.21192594X-RAY DIFFRACTION100
2.1239-2.1770.24861430.19892570X-RAY DIFFRACTION100
2.177-2.23590.25121390.19632597X-RAY DIFFRACTION100
2.2359-2.30170.24421260.18542632X-RAY DIFFRACTION100
2.3017-2.3760.24591330.18512602X-RAY DIFFRACTION100
2.376-2.46090.24661420.19282590X-RAY DIFFRACTION100
2.4609-2.55940.25431250.19522620X-RAY DIFFRACTION100
2.5594-2.67590.24211140.19342622X-RAY DIFFRACTION100
2.6759-2.81690.24661130.18312611X-RAY DIFFRACTION100
2.8169-2.99340.25311260.1952624X-RAY DIFFRACTION100
2.9934-3.22450.24721690.20022576X-RAY DIFFRACTION100
3.2245-3.54890.2161380.18282628X-RAY DIFFRACTION100
3.5489-4.06210.19911370.16692599X-RAY DIFFRACTION99
4.0621-5.11690.19691290.16672642X-RAY DIFFRACTION100
5.1169-46.97480.21281750.19292636X-RAY DIFFRACTION99
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)
12.35030.22210.30172.0375-0.40052.5195-0.0005-0.0089-0.24-0.0854-0.0706-0.06630.2630.0520.05440.1015-0.0050.02530.11130.00690.10635.6870.421125.2443
22.95991.22720.04520.5170.01071.2497-0.0919-0.1046-0.5638-0.07980.0342-0.36070.19590.09780.03880.15720.00750.04560.1810.04320.23823.3633-13.937534.4298
31.16740.04860.24680.9339-0.03351.478-0.03190.1947-0.3663-0.25560.10630.02330.29560.01660.0680.2358-0.05810.02060.1833-0.04210.222214.3739-14.738916.541
40.89380.76-0.18790.9095-0.2841.3005-0.12680.0562-0.079-0.12530.0875-0.0592-0.01610.06660.08730.1589-0.02490.02640.151-0.03850.163623.8781-1.792521.033
51.97410.0063-0.34481.88960.38332.25980.0490.00710.1835-0.0848-0.0474-0.0263-0.2216-0.04740.04860.08550.0020.00050.1072-0.00210.104534.1247-43.951625.0172
61.76690.8576-0.30251.46490.0951.660.01270.00570.52350.0075-0.00010.277-0.1831-0.206-0.00060.1603-0.0036-0.02440.207-0.05360.277946.417-29.47634.2306
72.48981.1295-1.06620.6708-0.46431.19140.08730.12410.7416-0.3110.15970.4406-0.87760.2035-0.13220.6545-0.0664-0.00780.3466-0.02310.623657.5489-17.474815.6754
80.6837-0.1064-0.32330.4949-0.14340.6457-0.29980.10690.311-0.45610.4075-0.1775-0.180.20970.26660.3265-0.25870.03050.21350.03370.200455.09-32.527215.0991
93.02581.7739-1.04662.00340.43951.52-0.08110.38010.2555-0.36090.1707-0.0526-0.25880.260.12990.2528-0.08530.04280.25340.01430.228150.9647-41.359911.9319
100.97710.8690.50811.53131.07371.5854-0.0003-0.0550.1137-0.0840.0096-0.0058-0.0572-0.05440.02230.1505-0.01590.01220.15550.02150.149643.0207-42.140825.9687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 71 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 72 THROUGH 117 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 118 THROUGH 219 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 220 THROUGH 332 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID -1 THROUGH 71 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 72 THROUGH 117 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 118 THROUGH 136 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 137 THROUGH 227 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 228 THROUGH 256 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 257 THROUGH 332 )

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