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- PDB-4zn2: Glycosyl hydrolase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4zn2
TitleGlycosyl hydrolase from Pseudomonas aeruginosa
ComponentsPslG
KeywordsHYDROLASE / biofilm / exopolysaccharides
Function / homology: / polysaccharide biosynthetic process / single-species biofilm formation / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / PslG
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSu, T. / Liu, S. / Gu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2015CB150600 China
CitationJournal: Cell Res. / Year: 2015
Title: PslG, a self-produced glycosyl hydrolase, triggers biofilm disassembly by disrupting exopolysaccharide matrix
Authors: Yu, S. / Su, T. / Wu, H. / Liu, S. / Wang, D. / Zhao, T. / Jin, Z. / Du, W. / Zhu, M.J. / Chua, S.L. / Yang, L. / Zhu, D. / Gu, L. / Ma, L.Z.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PslG
B: PslG
C: PslG
D: PslG


Theoretical massNumber of molelcules
Total (without water)189,0624
Polymers189,0624
Non-polymers00
Water29,2921626
1
A: PslG


Theoretical massNumber of molelcules
Total (without water)47,2661
Polymers47,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PslG


Theoretical massNumber of molelcules
Total (without water)47,2661
Polymers47,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PslG


Theoretical massNumber of molelcules
Total (without water)47,2661
Polymers47,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PslG


Theoretical massNumber of molelcules
Total (without water)47,2661
Polymers47,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.559, 88.206, 222.394
Angle α, β, γ (deg.)90.00, 96.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PslG / glycosyl hydrolase


Mass: 47265.535 Da / Num. of mol.: 4 / Fragment: UNP residues 31-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: pslG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I1N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1626 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3%(w/v) Dextran sulfate sodium salt, 0.1 M BICINE, 7%(w/v) PEG20000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 143014 / % possible obs: 99.4 % / Redundancy: 5.4 % / Rsym value: 0.122 / Net I/σ(I): 21.85
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.87 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
SCALEPACKdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.12 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2241 7234 5.06 %
Rwork0.1932 --
obs0.1954 142993 99.34 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.229 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3695 Å20 Å20.6728 Å2
2--5.5762 Å20 Å2
3----5.9457 Å2
Refinement stepCycle: LAST / Resolution: 2→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13316 0 0 1626 14942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613680
X-RAY DIFFRACTIONf_angle_d1.03118648
X-RAY DIFFRACTIONf_dihedral_angle_d14.6765036
X-RAY DIFFRACTIONf_chiral_restr0.0841972
X-RAY DIFFRACTIONf_plane_restr0.0052428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.03470.3383670.28466544X-RAY DIFFRACTION92
2.0347-2.07170.30443550.27386742X-RAY DIFFRACTION94
2.0717-2.11160.28463950.26146691X-RAY DIFFRACTION94
2.1116-2.15460.27283440.25566779X-RAY DIFFRACTION94
2.1546-2.20150.29623410.24466767X-RAY DIFFRACTION94
2.2015-2.25260.26893580.23776761X-RAY DIFFRACTION94
2.2526-2.30890.26293570.23196778X-RAY DIFFRACTION94
2.3089-2.37130.25773530.22746756X-RAY DIFFRACTION94
2.3713-2.44110.26423450.22556797X-RAY DIFFRACTION95
2.4411-2.51980.22793610.21876799X-RAY DIFFRACTION95
2.5198-2.60980.25643570.21666757X-RAY DIFFRACTION95
2.6098-2.71410.24833410.21026764X-RAY DIFFRACTION95
2.7141-2.83750.25753640.20286846X-RAY DIFFRACTION95
2.8375-2.98690.22283730.19796787X-RAY DIFFRACTION95
2.9869-3.17370.23053650.19626804X-RAY DIFFRACTION95
3.1737-3.41820.20993840.18466827X-RAY DIFFRACTION94
3.4182-3.76130.19273600.176817X-RAY DIFFRACTION95
3.7613-4.30330.18853590.14266858X-RAY DIFFRACTION95
4.3033-5.41330.14913680.13456842X-RAY DIFFRACTION94
5.4133-25.60270.2013240.1747048X-RAY DIFFRACTION95

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