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- PDB-5g5u: Crystal structure of NagZ H174A mutant from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5g5u
TitleCrystal structure of NagZ H174A mutant from Pseudomonas aeruginosa
ComponentsBETA-HEXOSAMINIDASE
KeywordsHYDROLASE / CELL-WALL RECYCLING / ANTIBIOTIC RESISTANCE / GLYCO 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
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionJun 5, 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 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,5012
Polymers76,5012
Non-polymers00
Water6,612367
1
A: BETA-HEXOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)38,2511
Polymers38,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-HEXOSAMINIDASE


Theoretical massNumber of molelcules
Total (without water)38,2511
Polymers38,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.231, 75.620, 76.720
Angle α, β, γ (deg.)90.00, 110.40, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL SEQUENCE CONTAINS A HIS-TAG FOR PURIFICATION. THERE IS A PUNCTUAL MUTATION AT ...THE EXPERIMENTAL SEQUENCE CONTAINS A HIS-TAG FOR PURIFICATION. THERE IS A PUNCTUAL MUTATION AT POSITION 174 (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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0 5 MM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015 / Details: KB MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.25→60.2 Å / Num. obs: 32273 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 22.69 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.7 / % possible all: 98.2

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Processing

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

Resolution: 2.25→60.202 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1658 5.1 %
Rwork0.1741 --
obs0.1771 32245 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→60.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 0 367 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085191
X-RAY DIFFRACTIONf_angle_d0.9867038
X-RAY DIFFRACTIONf_dihedral_angle_d18.8783154
X-RAY DIFFRACTIONf_chiral_restr0.051775
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31630.2491250.20132555X-RAY DIFFRACTION98
2.3163-2.3910.24491210.19012529X-RAY DIFFRACTION98
2.391-2.47650.26711290.19162580X-RAY DIFFRACTION99
2.4765-2.57560.2361330.19042551X-RAY DIFFRACTION99
2.5756-2.69290.30651560.19452513X-RAY DIFFRACTION99
2.6929-2.83480.24131410.1882566X-RAY DIFFRACTION99
2.8348-3.01240.26521430.18942534X-RAY DIFFRACTION98
3.0124-3.2450.28211440.18822555X-RAY DIFFRACTION99
3.245-3.57150.22411490.16872537X-RAY DIFFRACTION98
3.5715-4.08820.19171440.1492515X-RAY DIFFRACTION98
4.0882-5.15030.17851330.14682564X-RAY DIFFRACTION98
5.1503-60.22360.22741400.17452588X-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)
11.16410.23170.00961.57560.13021.7140.01880.03090.2255-0.0605-0.02780.0704-0.1816-0.01980.07620.0468-0.01270.01070.0566-0.00820.0889-24.8465-1.174897.1033
20.89250.2036-0.19090.6567-0.24051.1578-0.10.11650.3279-0.20280.1526-0.0288-0.26970.01960.01290.1845-0.09930.00690.152-0.01140.2215-6.01512.961392.8729
34.10852.0262-0.33771.31120.56021.7224-0.20420.31960.0515-0.23270.124-0.0073-0.14460.08480.13610.1529-0.06670.04650.1221-0.0070.1921-7.81931.239883.484
41.1930.58680.32851.50750.8881.89680.005-0.0650.0714-0.11230.06640.00570.00360.0002-0.03760.0754-0.01810.00480.08350.03110.1489-15.86810.482797.9492
51.92120.48210.22051.8252-0.2812.09090.00930.0023-0.21920.0157-0.0957-0.24640.21010.08750.05570.0832-0.01230.03010.08030.00440.1293-23.236443.295497.191
60.43770.12360.20971.34880.48291.9620.0385-0.0296-0.4022-0.03020.0382-0.0450.3114-0.0438-0.04340.1615-0.01890.03160.10720.01420.2761-38.958525.3893101.2081
71.1287-0.00740.25671.11410.07991.8907-0.00320.1559-0.2252-0.29170.06380.10020.25-0.11230.06130.1537-0.05570.00930.1259-0.0250.1713-44.237531.613287.5357
80.92740.2759-0.08551.1106-0.5962.097-0.04790.061-0.0513-0.11410.05260.0257-0.12180.10040.04590.0936-0.02640.02770.1145-0.03790.1617-34.226241.278893.9976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 71 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 72 THROUGH 227 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 228 THROUGH 256 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 257 THROUGH 332 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 0 THROUGH 71 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 72 THROUGH 136 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 137 THROUGH 227 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 228 THROUGH 332 )

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