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- PDB-3ckz: N1 Neuraminidase H274Y + Zanamivir -

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Basic information

Entry
Database: PDB / ID: 3ckz
TitleN1 Neuraminidase H274Y + Zanamivir
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE / N1 / Neuraminidase / H274Y / Zanamivir / Glycosidase / Membrane / Transmembrane / Virion
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 / identical protein binding / 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
ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsColllins, P. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2008
Title: Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants.
Authors: Collins, P.J. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity.src_method / _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_ptnr1_PDB_ins_code ..._chem_comp.type / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_conn.ptnr2_label_seq_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)42,5823
Polymers42,2101
Non-polymers3722
Water3,369187
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,32912
Polymers168,8404
Non-polymers1,4908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area15520 Å2
ΔGint-91.1 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.146, 115.146, 64.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

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Components

#1: Protein Neuraminidase /


Mass: 42209.941 Da / Num. of mol.: 1 / Fragment: UNP residues 63-447 / Mutation: H274Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Influenza A virus / Strain (production host): WSN-NA (H1N1) / References: UniProt: Q6DPL2, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-ZMR / ZANAMIVIR / MODIFIED SIALIC ACID / Zanamivir


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 30055 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→2 Å / % possible all: 61.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.34 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUE (A ASN 306 ) AND RESIDUE (A GLN 308 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.04. RESIDUE (A GLY 333 ) AND RESIDUE (A SER 335 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.85. ...Details: RESIDUE (A ASN 306 ) AND RESIDUE (A GLN 308 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.04. RESIDUE (A GLY 333 ) AND RESIDUE (A SER 335 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.85. RESIDUE (A CYS 336 ) AND RESIDUE (A GLY 339 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.97. RESIDUE (A SER 342 ) AND RESIDUE (A SER 344 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 2.07. RESIDUE (A VAL 392 ) AND RESIDUE (A LYS 394 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.76. RESIDUE (A GLU 433 ) AND RESIDUE (A SER 435 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.87.
RfactorNum. reflection% reflectionSelection details
Rfree0.22807 1614 5.1 %RANDOM
Rwork0.20106 ---
obs0.20249 30055 91.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 24 187 3175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223072
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9314174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0223.926135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74415465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg161516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022364
X-RAY DIFFRACTIONr_nbd_refined0.2490.21492
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.219
X-RAY DIFFRACTIONr_mcbond_it0.4621.51951
X-RAY DIFFRACTIONr_mcangle_it0.84323056
X-RAY DIFFRACTIONr_scbond_it1.38231331
X-RAY DIFFRACTIONr_scangle_it2.0514.51118
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 57 -
Rwork0.265 1279 -
obs--53.78 %

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