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- PDB-3o9j: Influenza NA in complex with compound 5 -

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Basic information

Entry
Database: PDB / ID: 3o9j
TitleInfluenza NA in complex with compound 5
ComponentsNeuraminidase
KeywordsHYDROLASE / Neuraminidase
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
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Chem-RP6 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.0002 Å
AuthorsRussell, R.J. / Kerry, P.S.
CitationJournal: Nat Commun / Year: 2010
Title: Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase.
Authors: Rudrawar, S. / Dyason, J.C. / Rameix-Welti, M.A. / Rose, F.J. / Kerry, P.S. / Russell, R.J. / van der Werf, S. / Thomson, R.J. / Naffakh, N. / von Itzstein, M.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_distant_solvent_atoms / pdbx_validate_chiral / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _entity.src_method / _pdbx_validate_chiral.auth_atom_id / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4324
Polymers42,8391
Non-polymers5933
Water5,765320
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,72716
Polymers171,3564
Non-polymers2,37012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area14680 Å2
ΔGint-109 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.580, 90.580, 109.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

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Components

#1: Protein Neuraminidase /


Mass: 42839.105 Da / Num. of mol.: 1 / Fragment: UNP Residues 81-467 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/duck/Ukraine/1/1963(H3N8))
Strain: A/Duck/Ukraine/1/1963 H3N8 / References: UniProt: Q07599, exo-alpha-sialidase
#2: Sugar ChemComp-RP6 / 5-acetamido-2,6-anhydro-3,5-dideoxy-3-prop-2-en-1-yl-D-glycero-D-galacto-non-2-enonic acid


Type: D-saccharide / Mass: 331.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H21NO8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 28298 / Num. obs: 27534 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 84.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0002→28.644 Å / SU ML: 0.33 / σ(F): 1.89 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1465 5.05 %Random
Rwork0.2148 ---
obs0.2182 27534 97.27 %-
all-28298 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.693 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3493 Å2-0 Å20 Å2
2---9.3493 Å2-0 Å2
3---18.6987 Å2
Refinement stepCycle: LAST / Resolution: 2.0002→28.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 39 320 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183127
X-RAY DIFFRACTIONf_angle_d1.8254237
X-RAY DIFFRACTIONf_dihedral_angle_d21.2931155
X-RAY DIFFRACTIONf_chiral_restr0.218456
X-RAY DIFFRACTIONf_plane_restr0.01546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.07170.37211220.27682393X-RAY DIFFRACTION84
2.0717-2.15460.36481350.25222666X-RAY DIFFRACTION94
2.1546-2.25260.29531600.23432774X-RAY DIFFRACTION100
2.2526-2.37130.34871610.22262806X-RAY DIFFRACTION100
2.3713-2.51980.26081650.21372806X-RAY DIFFRACTION100
2.5198-2.71420.30241530.19372811X-RAY DIFFRACTION100
2.7142-2.98710.28671300.19562822X-RAY DIFFRACTION99
2.9871-3.41880.28831430.19482806X-RAY DIFFRACTION99
3.4188-4.30490.24051690.18932812X-RAY DIFFRACTION99
4.3049-28.64680.23231270.21812833X-RAY DIFFRACTION98

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