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- PDB-2w38: Crystal structure of the pseudaminidase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 2w38
TitleCrystal structure of the pseudaminidase from Pseudomonas aeruginosa
ComponentsSIALIDASE
KeywordsTRANSFERASE / SIALIDASE / NEURAMINIDASE / PSEUDAMINIC ACID
Function / homology
Function and homology information


exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsXu, G. / Ryan, C. / Kiefel, M.J. / Wilson, J.C. / Taylor, G.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Studies on the Pseudomonas Aeruginosa Sialidase-Like Enzyme Pa2794 Suggest Substrate and Mechanistic Variations.
Authors: Xu, G. / Ryan, C. / Kiefel, M.J. / Wilson, J.C. / Taylor, G.L.
History
DepositionNov 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5605
Polymers47,1921
Non-polymers3684
Water7,494416
1
A: SIALIDASE
hetero molecules

A: SIALIDASE
hetero molecules

A: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,68115
Polymers141,5763
Non-polymers1,10512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area14120 Å2
ΔGint-64.3 kcal/mol
Surface area49290 Å2
MethodPQS
Unit cell
Length a, b, c (Å)126.200, 126.200, 126.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2046-

HOH

21A-2088-

HOH

31A-2241-

HOH

41A-2294-

HOH

51A-2353-

HOH

61A-2375-

HOH

71A-2377-

HOH

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Components

#1: Protein SIALIDASE / PSEUDAMINIDASE


Mass: 47192.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L6G4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.21 Å3/Da / Density % sol: 65 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 50018 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / % possible all: 70

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Processing

Software
NameClassification
ARP/wARPmodel building
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
DMphasing
ARP/wARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.9→33.74 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2543 5.1 %
Rwork0.175 --
obs0.176 49985 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.32 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 24 416 3725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133391
X-RAY DIFFRACTIONf_angle_d1.4744611
X-RAY DIFFRACTIONf_dihedral_angle_d17.4851131
X-RAY DIFFRACTIONf_chiral_restr0.106493
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93670.3066860.271571X-RAY DIFFRACTION56
1.9367-1.97620.28011110.23562000X-RAY DIFFRACTION72
1.9762-2.01920.23211300.22542366X-RAY DIFFRACTION87
2.0192-2.06610.24151400.21022597X-RAY DIFFRACTION94
2.0661-2.11780.26021430.19422716X-RAY DIFFRACTION98
2.1178-2.1750.20811300.19352767X-RAY DIFFRACTION100
2.175-2.2390.23331250.1892781X-RAY DIFFRACTION100
2.239-2.31130.21621560.17252752X-RAY DIFFRACTION100
2.3113-2.39390.21471720.17492765X-RAY DIFFRACTION100
2.3939-2.48970.19871430.16912755X-RAY DIFFRACTION100
2.4897-2.6030.20161650.16962773X-RAY DIFFRACTION100
2.603-2.74010.20581520.16992799X-RAY DIFFRACTION100
2.7401-2.91170.20841400.17572798X-RAY DIFFRACTION100
2.9117-3.13640.20291610.17172761X-RAY DIFFRACTION100
3.1364-3.45170.18561650.16382782X-RAY DIFFRACTION100
3.4517-3.95050.15981520.1542818X-RAY DIFFRACTION100
3.9505-4.97470.141470.12952827X-RAY DIFFRACTION99
4.9747-33.74440.17741250.17422814X-RAY DIFFRACTION95

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