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- PDB-5g6t: Crystal structure of Zn-containing NagZ H174A mutant from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 5g6t
TitleCrystal structure of Zn-containing NagZ H174A mutant from Pseudomonas aeruginosa
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCOSIDE HYDROLASE / N-ACETYLGLUCOSAMINIDASE / 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
DI(HYDROXYETHYL)ETHER / Beta-hexosaminidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionJul 15, 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 1.3May 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)76,7385
Polymers76,5012
Non-polymers2373
Water7,080393
1
A: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4223
Polymers38,2511
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3162
Polymers38,2511
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.095, 76.122, 76.005
Angle α, β, γ (deg.)90.00, 107.39, 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: 38250.605 Da / Num. of mol.: 2 / Mutation: YES
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. THE SEQUENCE INCLUDES THE SINGLE-POINT MUTATION H174A THAT MAKES THIS PROTEIN INACTIVE.
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZINC ION (ZN): THE SOURCE OF ZN IS UNKNOWN. IT IS LIKELY THAT ZN COMES EITHER THE EXPRESSION HOST ...ZINC ION (ZN): THE SOURCE OF ZN IS UNKNOWN. IT IS LIKELY THAT ZN COMES EITHER THE EXPRESSION HOST OR THE PURIFICATION BUFFERS DI(HYDROXYETHYL)ETHER (PEG): PEG IS PRESENT IN THE CRYSTALLIZATION CONDITION
Sequence detailsTHE EXPERIMENTAL SEQUENCE CONTAINS A HIS-TAG AT THE N- TERMINUS. THERE IS ALSO A SINGLE-POINT MUTATION H174A

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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: 2.07 Å3/Da / Density % sol: 40.8 % / 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: 0.97948
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.15→47.68 Å / Num. obs: 36891 / % possible obs: 97.2 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Biso Wilson estimate: 24.01 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.3
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

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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: 2.15→44.937 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML
Details: RESIDUES 124-135 AND 171-174 IN CHAIN A, AND REIDUES 124-134, 171-175 AND 249-251 IN CHAIN B WERE NOT MODELED DUE TO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2446 1817 4.9 %
Rwork0.1783 --
obs0.1816 36891 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 9 393 5242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084968
X-RAY DIFFRACTIONf_angle_d0.9926726
X-RAY DIFFRACTIONf_dihedral_angle_d19.4863028
X-RAY DIFFRACTIONf_chiral_restr0.053739
X-RAY DIFFRACTIONf_plane_restr0.006900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20820.31491260.25042700X-RAY DIFFRACTION97
2.2082-2.27310.3121500.23812666X-RAY DIFFRACTION97
2.2731-2.34650.30621620.22952674X-RAY DIFFRACTION97
2.3465-2.43040.31621460.21632696X-RAY DIFFRACTION97
2.4304-2.52770.26641150.2172727X-RAY DIFFRACTION97
2.5277-2.64270.27191480.19892655X-RAY DIFFRACTION97
2.6427-2.7820.271490.19072701X-RAY DIFFRACTION97
2.782-2.95630.281510.19372676X-RAY DIFFRACTION97
2.9563-3.18450.26871120.18322736X-RAY DIFFRACTION97
3.1845-3.50480.26441230.16952707X-RAY DIFFRACTION97
3.5048-4.01170.19941320.14512689X-RAY DIFFRACTION95
4.0117-5.05320.18051440.13592684X-RAY DIFFRACTION96
5.0532-44.94630.1971590.15742763X-RAY DIFFRACTION97
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)
12.77050.3368-0.44662.74021.11223.77550.03750.15730.1458-0.1117-0.10730.14410.0119-0.15740.05460.0972-0.0107-0.02820.11470.00390.1574-19.2891-2.335497.8346
20.4637-0.5407-0.87781.57340.1352.5014-0.18730.06370.3743-0.13370.08660.4304-0.1387-0.16290.05860.21370.0137-0.08690.17850.00690.2582-8.59916.5562107.9928
30.21860.2794-0.26310.8220.3933.1612-0.09520.20650.1436-0.21210.1863-0.0528-0.49310.2233-0.05840.257-0.0814-0.01670.24910.04090.17651.057911.308789.7134
40.64150.41550.17651.09630.96422.2785-0.04530.0940.1021-0.1350.02490.0741-0.0446-0.03990.07120.13910.0083-0.0190.15740.0430.1742-8.04582.104695.2007
52.31470.10480.80082.6493-1.18923.8679-0.02470.0782-0.0452-0.0414-0.0735-0.09060.01620.07470.09780.09190.00680.00780.11590.02160.1363-16.931447.519197.7584
61.00340.73130.82192.7262-0.07831.3026-0.1880.2204-0.3934-0.10880.1754-0.34360.0780.06580.01760.2374-0.00530.0670.1984-0.01980.2452-27.478528.718107.8666
70.7347-0.3170.60051.11090.03783.36240.06770.0794-0.1632-0.2153-0.00750.13540.4681-0.1091-0.02040.2476-0.0410.00350.1756-0.01690.1661-36.931532.910590.728
80.60920.4216-0.21031.1187-0.44871.8863-0.0423-0.01170.0026-0.07050.0001-0.0731-0.04620.03240.07830.117-0.00290.02360.125-0.0270.1327-29.173943.286694.1803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 62 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 63 THROUGH 107 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 108 THROUGH 227 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 228 THROUGH 332 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 0 THROUGH 62 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 63 THROUGH 107 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 108 THROUGH 219 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 220 THROUGH 332 )

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