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- PDB-5ly7: Crystal structure of NagZ H174A mutant from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 5ly7
TitleCrystal structure of NagZ H174A mutant from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin
ComponentsBeta-hexosaminidase
KeywordsGENE REGULATION / Cell-Wall Recycling Beta-hexosaminidase Pseudomonas aeruginosa Inhibitor
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / peptidoglycan turnover / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / 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 ...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 / DI(HYDROXYETHYL)ETHER / 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
DepositionSep 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 1.3May 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)77,1226
Polymers76,5012
Non-polymers6214
Water27015
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5613
Polymers38,2511
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5613
Polymers38,2511
Non-polymers3102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.140, 66.930, 74.060
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: -1 - 332 / Label seq-ID: 20 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta-hexosaminidase / Beta-N-acetylhexosaminidase / N-acetyl-beta-glucosaminidase


Mass: 38250.605 Da / Num. of mol.: 2 / Mutation: H174A
Source method: isolated from a genetically manipulated source
Details: There is a single-point mutation at His174, H174A / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: nagZ, PA3005 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZK0, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NOK / 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 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: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2015
RadiationMonochromator: SI(111) Channel.cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.1→73.23 Å / Num. obs: 10753 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.929 / Rmerge(I) obs: 0.182 / Rsym value: 0.146 / Net I/σ(I): 4.2
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.75 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystallographic structure of NagZ from Pseudomonas aeruginosa

Resolution: 3.1→73.23 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.819 / SU B: 31.324 / SU ML: 0.542 / Cross valid method: THROUGHOUT / ESU R Free: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 565 5.3 %RANDOM
Rwork0.21684 ---
obs0.22069 10175 92.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.773 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å21.53 Å2
2---2.99 Å20 Å2
3----1.69 Å2
Refinement stepCycle: 1 / Resolution: 3.1→73.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 42 15 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195227
X-RAY DIFFRACTIONr_bond_other_d0.0030.025092
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9687073
X-RAY DIFFRACTIONr_angle_other_deg1.963311627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47322.632247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19615845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9781563
X-RAY DIFFRACTIONr_chiral_restr0.0690.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it22.0721.0462662
X-RAY DIFFRACTIONr_mcbond_other21.9951.0432661
X-RAY DIFFRACTIONr_mcangle_it21.0261.6813321
X-RAY DIFFRACTIONr_mcangle_other21.0591.6833322
X-RAY DIFFRACTIONr_scbond_it32.7051.8632565
X-RAY DIFFRACTIONr_scbond_other32.6921.8642565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other29.7482.3953752
X-RAY DIFFRACTIONr_long_range_B_refined28.00614.9635704
X-RAY DIFFRACTIONr_long_range_B_other28.00614.9665705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21880 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 35 -
Rwork0.295 731 -
obs--93.99 %

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