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- PDB-1nna: THREE-DIMENSIONAL STRUCTURE OF INFLUENZA A N9 NEURAMINIDASE AND I... -

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Basic information

Entry
Database: PDB / ID: 1nna
TitleTHREE-DIMENSIONAL STRUCTURE OF INFLUENZA A N9 NEURAMINIDASE AND ITS COMPLEX WITH THE INHIBITOR 2-DEOXY 2,3-DEHYDRO-N-ACETYL NEURAMINIC ACID
ComponentsNEURAMINIDASE
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBossart-Whitaker, P. / Carson, M. / Babu, Y.S. / Smith, C.D. / Laver, W.G. / Air, G.M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid.
Authors: Bossart-Whitaker, P. / Carson, M. / Babu, Y.S. / Smith, C.D. / Laver, W.G. / Air, G.M.
#1: Journal: Thesis / Year: 1992
Title: Three-Dimensional Structure of Influenza A(Slash)Tern(Slash)Australia(Slash)G70C(Slash)75 N9 Neuraminidase and its Complex with the Inhibitor 2-Deoxy-2,3-Dehydro N-Acetyl Neuraminic Acid
Authors: Bossart-Whitaker, P.J.
#2: Journal: Virology / Year: 1991
Title: Transfer of the Hemagglutinin Activity of Influenza Virus Neuraminidase Subtype N9 Into an N2 Background
Authors: Nuss, J.M. / Air, G.M.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
Authors: Tulip, W.R. / Varghese, J.N. / Baker, A.T. / Van Donkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#4: Journal: Proteins / Year: 1987
Title: Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus
Authors: Baker, A.T. / Varghese, J.N. / Laver, W.G. / Air, G.M. / Colman, P.M.
#5: Journal: Virology / Year: 1985
Title: Gene and Protein Sequence of an Influenza Neuraminidase with Hemagglutinin Activity
Authors: Air, G.M. / Ritchie, L.R. / Laver, W.G. / Colman, P.M.
#6: Journal: Virology / Year: 1984
Title: Influenza Virus Neuraminidase with Hemagglutinin Activity
Authors: Laver, W.G. / Colman, P.M. / Webster, R.G. / Hinshaw, V.S.
#7: Journal: Bull.Who. / Year: 1980
Title: Memorandum: A Revision of the System of Nomenclature for Influenza Viruses
History
DepositionMar 8, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET STRAND 1 OF SHEET S3 (LEU 225 - HIS 235) IS NOT REALLY PART OF THE SHEET BY H-BONDING ...SHEET STRAND 1 OF SHEET S3 (LEU 225 - HIS 235) IS NOT REALLY PART OF THE SHEET BY H-BONDING CRITERIA BECAUSE IT IS IN AN EXTENDED CONFORMATION. OTHERS HAVE BEEN INCLUDED IN THE SHEET MOSTLY FOR THE SAKE OF SYMMETRY; I.E., THE STRUCTURE THEN CONSISTS OF SIX SHEETS OF FOUR ANTIPARALLEL STRANDS EACH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6072
Polymers43,5671
Non-polymers401
Water0
1
A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4278
Polymers174,2664
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area13310 Å2
ΔGint-96 kcal/mol
Surface area45690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)183.780, 183.780, 183.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Atom site foot note1: CIS PROLINE - PRO 328 / 2: CIS PROLINE - PRO 433

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Components

#1: Protein NEURAMINIDASE /


Mass: 43566.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: A/Tern/Australia/G70C/75 H11N9 / Cell line: S2 / References: UniProt: P03472, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→6 Å
Details: RESIDUE 336 IS GLY. IT WAS REFINED AS ASN AND THE AUTHORS NOTED THAT THE SIDE CHAIN OF THIS RESIDUE NEVER DISPLAYED DENSITY (SEE FIGURE 3A OF THE PAPER CITED ON *JRNL* RECORDS ABOVE). THE ...Details: RESIDUE 336 IS GLY. IT WAS REFINED AS ASN AND THE AUTHORS NOTED THAT THE SIDE CHAIN OF THIS RESIDUE NEVER DISPLAYED DENSITY (SEE FIGURE 3A OF THE PAPER CITED ON *JRNL* RECORDS ABOVE). THE AUTHORS BELIEVE THAT CHANGING IT TO GLY WILL HAVE A NEGLIGIBLE EFFECT ON THE REST OF THE STRUCTURE.
RfactorNum. reflection
Rwork0.193 -
obs0.193 14296
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 1 0 3057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.6

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