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- PDB-3k3a: Crystal Structure of B/Perth Neuraminidase D197E mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 3k3a
TitleCrystal Structure of B/Perth Neuraminidase D197E mutant in complex with Oseltamivir
ComponentsNeuraminidase
KeywordsHYDROLASE / INFLUENZA / NEURAMINIDASE / MUTATION / RESISTANCE / TAMIFLU / Oseltamivir / GS-4071 / 196618-13-0 / Cell membrane / Glycosidase / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / YTTRIUM (III) ION / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsOakley, A.J. / McKimm-Breschkin, J.L.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses.
Authors: Oakley, A.J. / Barrett, S. / Peat, T.S. / Newman, J. / Streltsov, V.A. / Waddington, L. / Saito, T. / Tashiro, M. / McKimm-Breschkin, J.L.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
I: Neuraminidase
J: Neuraminidase
K: Neuraminidase
L: Neuraminidase
M: Neuraminidase
N: Neuraminidase
O: Neuraminidase
P: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)710,50868
Polymers701,42216
Non-polymers9,08652
Water11,440635
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,62717
Polymers175,3554
Non-polymers2,27113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15180 Å2
ΔGint-75 kcal/mol
Surface area45430 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,62717
Polymers175,3554
Non-polymers2,27113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-76 kcal/mol
Surface area45480 Å2
MethodPISA
3
I: Neuraminidase
J: Neuraminidase
K: Neuraminidase
L: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,62717
Polymers175,3554
Non-polymers2,27113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15140 Å2
ΔGint-75 kcal/mol
Surface area45390 Å2
MethodPISA
4
M: Neuraminidase
N: Neuraminidase
O: Neuraminidase
P: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,62717
Polymers175,3554
Non-polymers2,27113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15100 Å2
ΔGint-76 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.802, 123.836, 123.967
Angle α, β, γ (deg.)90.04, 90.17, 90.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 78 - 262 / Label seq-ID: 9 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 32 molecules ABCDEFGHIJKLMNOP

#1: Protein
Neuraminidase


Mass: 43838.863 Da / Num. of mol.: 16 / Fragment: UNP residues 70-466 / Mutation: D197E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Perth/211/2001 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q3S340, exo-alpha-sialidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 671 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate


Mass: 284.351 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication*YM
#5: Chemical
ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Y
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K, PH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2008 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.323
11-H, K, -L20.224
11H, -L, K30.097
11-h,-k,l40.1
11-H, L, K50.256
ReflectionResolution: 2.25→50 Å / Num. all: 289650 / Num. obs: 289650 / % possible obs: 91.8 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2 % / Biso Wilson estimate: 29.746 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1 / Num. unique all: 29350 / % possible all: 63.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K38

3k38


Resolution: 2.59→49.69 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.53 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 9843 4.9 %RANDOM
Rwork0.20689 ---
obs0.20796 189381 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.491 Å2
Baniso -1Baniso -2Baniso -3
1-73.42 Å24.97 Å2-7.75 Å2
2---49.93 Å230.06 Å2
3----23.49 Å2
Refinement stepCycle: LAST / Resolution: 2.59→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47984 0 564 635 49183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02149840
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.611.96167456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98556208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80423.3332064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.695158256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.94415304
X-RAY DIFFRACTIONr_chiral_restr0.1040.27152
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02137680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.391.530736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.681249280
X-RAY DIFFRACTIONr_scbond_it1.39319104
X-RAY DIFFRACTIONr_scangle_it2.124.518176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3053 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.060.05
Btight positional0.060.05
Ctight positional0.060.05
Dtight positional0.050.05
Etight positional0.060.05
Ftight positional0.060.05
Gtight positional0.060.05
Htight positional0.060.05
Itight positional0.060.05
Jtight positional0.060.05
Ktight positional0.060.05
Ltight positional0.060.05
Mtight positional0.060.05
Ntight positional0.060.05
Otight positional0.060.05
Ptight positional0.060.05
Atight thermal0.130.5
Btight thermal0.130.5
Ctight thermal0.120.5
Dtight thermal0.120.5
Etight thermal0.120.5
Ftight thermal0.120.5
Gtight thermal0.120.5
Htight thermal0.120.5
Itight thermal0.130.5
Jtight thermal0.130.5
Ktight thermal0.130.5
Ltight thermal0.130.5
Mtight thermal0.130.5
Ntight thermal0.130.5
Otight thermal0.130.5
Ptight thermal0.130.5
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 666 -
Rwork0.328 11921 -
obs--82.13 %

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