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- PDB-3h6j: Crystal structure of a putative neuraminidase from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 3h6j
TitleCrystal structure of a putative neuraminidase from Pseudomonas aeruginosa
ComponentsNeuraminidase
KeywordsHYDROLASE / SIX-BLADED BETA-PROPELLER / CELL WALL / GLYCOSIDASE / PEPTIDOGLYCAN-ANCHOR / SECRETED
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
: / PA2794-like, C-terminal / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like fold ...: / PA2794-like, C-terminal / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHsiao, Y.-S. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structures of respiratory pathogen neuraminidases
Authors: Hsiao, Y.-S. / Parker, D. / Ratner, A.J. / Prince, A. / Tong, L.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase


Theoretical massNumber of molelcules
Total (without water)47,1581
Polymers47,1581
Non-polymers00
Water16,358908
1
A: Neuraminidase

A: Neuraminidase

A: Neuraminidase


Theoretical massNumber of molelcules
Total (without water)141,4743
Polymers141,4743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area14910 Å2
ΔGint-68 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.340, 126.340, 126.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Neuraminidase / Sialidase


Mass: 47157.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2794 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Star / References: UniProt: Q9L6G4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes, 5% Tacsimate, 7% (w/v) PEGMME 5000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2006 / Details: Mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 88080 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.8493
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.299 / Num. unique all: 8684 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.94 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 439616.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 6447 7.6 %RANDOM
Rwork0.172 ---
all0.172 ---
obs0.172 85363 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7778 Å2 / ksol: 0.348456 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 0 908 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.362
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.182.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.237 593 7.4 %
Rwork0.217 7441 -
obs-7441 91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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