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- PDB-3k38: Crystal Structure of B/Perth Neuraminidase D197E mutant -

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Basic information

Entry
Database: PDB / ID: 3k38
TitleCrystal Structure of B/Perth Neuraminidase D197E mutant
ComponentsNeuraminidase
KeywordsHYDROLASE / INFLUENZA / NEURAMINIDASE / MUTATION / RESISTANCE / 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
YTTRIUM (III) ION / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 1.2Nov 15, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Jul 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 1.4Nov 10, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Nov 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 1.6Oct 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)708,91884
Polymers701,42216
Non-polymers7,49668
Water23,4921304
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,22921
Polymers175,3554
Non-polymers1,87417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19120 Å2
ΔGint-225 kcal/mol
Surface area45030 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,22921
Polymers175,3554
Non-polymers1,87417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-228 kcal/mol
Surface area45160 Å2
MethodPISA
3
I: Neuraminidase
J: Neuraminidase
K: Neuraminidase
L: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,22921
Polymers175,3554
Non-polymers1,87417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-228 kcal/mol
Surface area45070 Å2
MethodPISA
4
M: Neuraminidase
N: Neuraminidase
O: Neuraminidase
P: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,22921
Polymers175,3554
Non-polymers1,87417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-227 kcal/mol
Surface area45140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.155, 123.683, 123.789
Angle α, β, γ (deg.)90.04, 90.19, 90.19
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: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 78 - 466 / Label seq-ID: 9 - 397

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

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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, 1356 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Y
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K, PH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 22, 2008 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.415
11-H, -L, -K20.049
11-H, K, -L30.137
11-h,-k,l40.096
11h,-k,-l50.226
11-H, L, K60.076
ReflectionResolution: 2.19→61.78 Å / Num. all: 316772 / Num. obs: 316772 / % possible obs: 94.6 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.6 / Num. unique all: 45355 / % possible all: 92.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K36

3k36


Resolution: 2.19→61.78 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.46 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21989 16084 5 %RANDOM
Rwork0.19101 ---
obs0.19247 300686 93.25 %-
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: 13.721 Å2
Baniso -1Baniso -2Baniso -3
1-39.01 Å2-2.04 Å26.79 Å2
2---17.59 Å2-2.21 Å2
3----21.42 Å2
Refinement stepCycle: LAST / Resolution: 2.19→61.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48112 0 340 1304 49756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02250464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.95668496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09856464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39223.3832128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.277158496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4715320
X-RAY DIFFRACTIONr_chiral_restr0.1030.27232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02138400
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_it0.5851.531216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.882250208
X-RAY DIFFRACTIONr_scbond_it1.698319248
X-RAY DIFFRACTIONr_scangle_it2.1634.518192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3067 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.10.5
2Bmedium positional0.110.5
3Cmedium positional0.10.5
4Dmedium positional0.10.5
5Emedium positional0.110.5
6Fmedium positional0.10.5
7Gmedium positional0.10.5
8Hmedium positional0.10.5
9Imedium positional0.10.5
10Jmedium positional0.10.5
11Kmedium positional0.10.5
12Lmedium positional0.10.5
13Mmedium positional0.10.5
14Nmedium positional0.10.5
15Omedium positional0.10.5
16Pmedium positional0.110.5
1Amedium thermal0.762
2Bmedium thermal0.822
3Cmedium thermal0.772
4Dmedium thermal0.822
5Emedium thermal0.772
6Fmedium thermal0.762
7Gmedium thermal0.772
8Hmedium thermal0.742
9Imedium thermal0.822
10Jmedium thermal0.772
11Kmedium thermal0.812
12Lmedium thermal0.752
13Mmedium thermal0.772
14Nmedium thermal0.732
15Omedium thermal0.752
16Pmedium thermal0.752
LS refinement shellResolution: 2.189→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 1015 -
Rwork0.249 17899 -
obs--75.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1724-0.0922-0.34040.47220.00620.7258-0.0067-0.02310.01350.110.01080.0316-0.0225-0.0122-0.00410.0745-0.01680.02240.0665-0.05760.0471-0.05998.705926.4684
20.2733-0.27090.24560.8561-0.06310.4453-0.00770.00390.0401-0.0147-0.01110.0122-0.0429-0.05320.01880.063-0.02450.03790.0494-0.03560.0525-0.327626.5619-8.8355
30.33450.17070.24880.5420.02690.78060.00320.073-0.0142-0.1037-0.00040.0644-0.0038-0.024-0.00280.0915-0.01340.01950.0503-0.04090.041-0.0074-8.897-26.5582
40.24910.319-0.18790.8019-0.13490.52070.00250.0106-0.04290.011-0.01190.01170.0065-0.06750.00940.0682-0.00810.01760.0456-0.0420.0545-0.2545-26.73968.9017
50.3051-0.06330.27640.5263-0.13730.7730.0103-0.04990.02290.0872-0.0062-0.0076-0.0295-0.0581-0.00410.0768-0.01750.03150.0629-0.05730.0583-12.841366.4287-34.1719
60.3249-0.2622-0.01540.8289-0.02260.74180.0263-0.0087-0.06320.01420.00030.01220.1168-0.0036-0.02660.0733-0.03530.01570.0752-0.04890.0489-12.410134.1654-57.2963
70.35470.0919-0.19370.65760.01310.78490.02150.0643-0.0167-0.0797-0.0118-0.00430.0362-0.0265-0.00980.0677-0.00790.01320.0556-0.05250.0529-12.614757.2967-89.561
80.3560.22320.01260.8410.03020.67220.01430.02360.04560.0131-0.0020.0268-0.1018-0.0046-0.01220.0815-0.0020.02830.0682-0.04270.0434-12.518589.601-66.445
90.2194-0.2242-0.11210.64040.05170.51350.00930.013-0.0379-0.0186-0.0159-0.02150.03990.0750.00660.065-0.02260.03120.0399-0.03810.046243.281335.4021-8.6528
100.44270.1459-0.29880.6672-0.14010.74740.00110.04870.0006-0.10080.01-0.05580.00320.0388-0.01110.0772-0.00830.01830.0494-0.04210.039443.176470.742-26.4959
110.46120.31860.17440.70550.01720.48270.00220.01690.02170.0325-0.0077-0.0065-0.03250.05620.00550.0622-0.01990.02680.0381-0.04190.047443.133488.36028.9386
120.3339-0.27110.29130.6612-0.22030.74460.0005-0.0406-0.00280.09740.0107-0.05690.0040.0123-0.01120.089-0.0320.02010.0519-0.04260.044543.082552.908726.7496
130.2329-0.07-0.24710.6316-0.07430.79020.0058-0.032-0.01510.0856-0.0040.0210.01430.0286-0.00190.0638-0.0190.01490.0582-0.05120.0519-55.057-4.6306-34.1855
140.3049-0.31180.07060.802-0.19210.71270.0165-0.00780.03020.0187-0.0032-0.0262-0.1309-0.0002-0.01330.0824-0.03240.03010.0743-0.06280.0511-55.357827.649-57.2858
150.38020.11210.22750.6084-0.01760.80650.01540.02050.0341-0.0907-0.02340.0144-0.01610.04020.00790.0719-0.01520.03120.0482-0.04490.0511-54.93694.5986-89.566
160.41610.2501-0.02570.7893-0.13880.76920.01880.0039-0.0238-0.0190.0125-0.01230.11490.008-0.03130.0851-0.00250.0120.0644-0.05590.0491-55.1905-27.733-66.46
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 466
2X-RAY DIFFRACTION2B78 - 466
3X-RAY DIFFRACTION3C78 - 466
4X-RAY DIFFRACTION4D78 - 466
5X-RAY DIFFRACTION5E78 - 466
6X-RAY DIFFRACTION6F78 - 466
7X-RAY DIFFRACTION7G78 - 466
8X-RAY DIFFRACTION8H78 - 466
9X-RAY DIFFRACTION9I78 - 466
10X-RAY DIFFRACTION10J78 - 466
11X-RAY DIFFRACTION11K78 - 466
12X-RAY DIFFRACTION12L78 - 466
13X-RAY DIFFRACTION13M78 - 466
14X-RAY DIFFRACTION14N78 - 466
15X-RAY DIFFRACTION15O78 - 466
16X-RAY DIFFRACTION16P78 - 466

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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