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- PDB-4mss: Crystal structure of Burkholderia cenocepacia family 3 glycoside ... -

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Basic information

Entry
Database: PDB / ID: 4mss
TitleCrystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to (3S,4R,5R,6S)-3-acetamido-4,5,6-trihydroxyazepane
ComponentsBeta-hexosaminidase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TIM barrel / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / : / 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
Chem-2CZ / Beta-hexosaminidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVadlamani, G. / Mark, B.L.
CitationJournal: Chem.Commun.(Camb.) / Year: 2013
Title: Selective trihydroxyazepane NagZ inhibitors increase sensitivity of Pseudomonas aeruginosa to beta-lactams.
Authors: Mondon, M. / Hur, S. / Vadlamani, G. / Rodrigues, P. / Tsybina, P. / Oliver, A. / Mark, B.L. / Vocadlo, D.J. / Bleriot, Y.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 1
B: Beta-hexosaminidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9187
Polymers76,2342
Non-polymers6855
Water14,790821
1
A: Beta-hexosaminidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4133
Polymers38,1171
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5054
Polymers38,1171
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.760, 87.580, 67.210
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-hexosaminidase 1 / Family 3 Glycoside hydrolase / NagZ / Beta-hexosaminidase 2


Mass: 38116.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656
Gene: BCAL1010, BCAL2860, BceJ2315_10000, BceJ2315_27960, nagZ, nagZ1, nagZ2
Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EA43, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-2CZ / N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide


Mass: 204.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16N2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 30% PEG8000, 0.1 M MES, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2013 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.59 Å / Num. all: 51229 / Num. obs: 51148 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.552 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(dev_1320)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GNV

4gnv


Resolution: 1.8→27.19 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.47 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 1317 2.58 %RANDOM
Rwork0.135 ---
all-51229 --
obs-51127 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→27.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 46 821 5965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015242
X-RAY DIFFRACTIONf_angle_d1.3447122
X-RAY DIFFRACTIONf_dihedral_angle_d12.2481872
X-RAY DIFFRACTIONf_chiral_restr0.07836
X-RAY DIFFRACTIONf_plane_restr0.007924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.27631380.2275429X-RAY DIFFRACTION96
1.8721-1.95720.27711380.19185409X-RAY DIFFRACTION96
1.9572-2.06040.22221540.15635424X-RAY DIFFRACTION97
2.0604-2.18940.21621450.13655483X-RAY DIFFRACTION97
2.1894-2.35840.18091390.12945513X-RAY DIFFRACTION98
2.3584-2.59560.18791490.12645587X-RAY DIFFRACTION98
2.5956-2.97070.18841520.1325587X-RAY DIFFRACTION99
2.9707-3.74130.19311520.12025654X-RAY DIFFRACTION99
3.7413-27.1930.14431500.12065724X-RAY DIFFRACTION100

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