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- PDB-7cm1: Neuraminidase from the Wuhan Asiatic toad influenza virus -

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Basic information

Entry
Database: PDB / ID: 7cm1
TitleNeuraminidase from the Wuhan Asiatic toad influenza virus
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE / Lattice-translocation defects LTD Neuraminidase NA
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesWuhan asiatic toad influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWang, J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Lattice-translocation defects in specific crystals of the catalytic head domain of influenza neuraminidase.
Authors: Li, L. / Dai, S. / Gao, G.F. / Wang, J.
History
DepositionJul 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neuraminidase
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6206
Polymers83,9712
Non-polymers6494
Water13,313739
1
B: Neuraminidase
A: Neuraminidase
hetero molecules

B: Neuraminidase
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,24012
Polymers167,9434
Non-polymers1,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area11800 Å2
ΔGint-40 kcal/mol
Surface area46310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.966, 143.148, 120.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein Neuraminidase / Toad NA


Mass: 41985.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuhan asiatic toad influenza virus / Gene: NA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A2P1GNT2, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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.: 2 / Source method: isolated from a natural source / Formula: C14H24N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 8 mg/mL in 20 mM Tris, 50 mM NaCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 55993 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.2
Reflection shellResolution: 2.14→2.22 Å / Num. unique obs: 5151 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIXdev_3940refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9S

1b9s


Resolution: 2.14→18.35 Å / SU ML: 0.3356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2796 2766 4.95 %
Rwork0.2204 53092 -
obs0.2234 55858 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.77 Å2
Refinement stepCycle: LAST / Resolution: 2.14→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 42 739 6625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755988
X-RAY DIFFRACTIONf_angle_d0.99438114
X-RAY DIFFRACTIONf_chiral_restr0.0553928
X-RAY DIFFRACTIONf_plane_restr0.00661050
X-RAY DIFFRACTIONf_dihedral_angle_d21.75322228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.180.34931280.26182506X-RAY DIFFRACTION93.4
2.18-2.220.32571420.27722624X-RAY DIFFRACTION98.54
2.22-2.260.37531430.2852639X-RAY DIFFRACTION99.07
2.26-2.310.34951420.26862672X-RAY DIFFRACTION99.15
2.31-2.360.32341190.27612655X-RAY DIFFRACTION98.93
2.36-2.410.34621460.26192665X-RAY DIFFRACTION99.26
2.41-2.470.34271290.26172671X-RAY DIFFRACTION99.36
2.47-2.540.31541420.25642671X-RAY DIFFRACTION99.5
2.54-2.610.31041280.25072671X-RAY DIFFRACTION98.8
2.61-2.70.35741160.24862670X-RAY DIFFRACTION99.43
2.7-2.790.321650.24012651X-RAY DIFFRACTION98.74
2.79-2.90.34131460.23692656X-RAY DIFFRACTION99.08
2.9-3.040.27691240.22512693X-RAY DIFFRACTION98.63
3.04-3.20.24411350.21482636X-RAY DIFFRACTION97.95
3.2-3.390.26641500.20372645X-RAY DIFFRACTION97.8
3.39-3.650.27251450.20232645X-RAY DIFFRACTION97.11
3.65-4.020.23821250.18312658X-RAY DIFFRACTION97.27
4.02-4.590.21821320.17182662X-RAY DIFFRACTION96.95
4.59-5.760.21011490.17852663X-RAY DIFFRACTION96.63
5.76-18.350.23991600.20822739X-RAY DIFFRACTION96.31
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)
10.242591720567-0.1930920789240.178780023720.276730206839-0.2545659967940.880286187469-0.001000715457090.0288273383972-0.0485471582250.03644329275750.03209634376950.0771294767126-0.0720230166444-0.100695126551-0.02718732492190.1604811026650.006713625627130.007607061161320.2019584235460.00475405959110.175132883335-17.874973732918.6544848113-33.9089159559
22.936117614690.578322073424-1.023992357193.61388362895-2.010401105453.18183623974-0.0632102783558-0.0217879865293-0.0516153225931-0.08303919715070.02129870664340.366388060487-0.0596778189036-0.2597209142630.0008742892072260.1557767814250.0239168982962-0.009805091140810.194657894417-0.01963642059930.159248892381-33.714826910322.9858199999-31.8521067243
32.58639144398-0.0690601120624-0.4827039462682.47287463622-1.065354248082.24118180999-0.1652284496450.02922710955680.119897630611-0.09724714608430.1595137011720.5653803780150.110614393092-0.195091037396-0.02365559776920.1488496440340.03002498696130.007129669755990.2349077773470.03692313180820.204962933754-35.379752291428.9522385058-32.1769618713
40.3835747097660.2158958375650.704742699461.121480789990.3874591818931.257520187920.03091363348070.09043507349510.135571615513-0.0761813620478-0.06972966461930.2303933671430.0977216335181-0.1392309831560.045775249780.1465667475390.0211429954543-0.01497120032720.290196378829-0.02246974845220.260597646821-36.579530228723.3974399791-47.0523514033
51.92551171487-1.203886777310.7972795887881.47590942586-0.8174374975721.390537948630.1295228329760.245526215516-0.0337645773149-0.177323467949-0.1352472931120.1785068241150.03036188796690.0113558083446-0.00442535215540.1752066726430.00133232604152-0.02305927596930.195394095579-0.02563892267280.147337629509-22.8178801516.5136282018-51.3811110739
60.7884209761390.209006658113-0.1718028486930.9852141885320.9410920437171.14139634114-0.0174814793352-0.0162991133934-0.0177779888626-0.0004846329531640.04089093702890.04190002209-0.0555484095527-0.0639091850114-0.03497159903890.1385889396710.0273113054653-0.0103536649610.1438277082720.01409222604850.133636717814-6.4858231064917.4028228253-14.1787955401
73.081995606-1.351928421380.06417520491222.429381951480.6171453333341.03579377133-0.0148516578988-0.129606183275-0.1568290842160.128733725730.02674540169390.140947167494-0.07211940896690.0176430954611-0.02335471247730.137343061761-0.007101536198930.004909593782310.1770167361-0.009857223275220.1266730645490.77075290548625.10306384341.76459354634
81.073903700481.07576927582-0.7988479732952.0429836081-0.6823566524160.6045288476430.102050297568-0.113916945861-0.0409662330860.310692453445-0.0511193299255-0.003562509864-0.0688800068257-0.0944124206749-0.05186972117320.2229337237350.008784017396330.0006236567517150.2948910249150.00620392757280.177961723219-16.970990601923.49949065866.47005761188
90.786048330937-0.555385743154-0.6366498398161.217571486541.17747398692.61483182550.0275624970044-0.06627316102470.02351697282630.138455741447-0.1154008476670.0861557601353-0.0364210805803-0.2672721863370.08780247829040.113984262207-0.01293916318940.00696990987020.2220967660350.01347244304090.167995368838-21.338722542116.6342541579-7.2876165743
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 80 through 214 )BA80 - 2141 - 135
22chain 'B' and (resid 215 through 250 )BA215 - 250136 - 171
33chain 'B' and (resid 251 through 277 )BA251 - 277172 - 198
44chain 'B' and (resid 278 through 362 )BA278 - 362199 - 283
55chain 'B' and (resid 363 through 466 )BA363 - 466284 - 387
66chain 'A' and (resid 80 through 186 )AD80 - 1861 - 107
77chain 'A' and (resid 187 through 277 )AD187 - 277108 - 198
88chain 'A' and (resid 278 through 362 )AD278 - 362199 - 283
99chain 'A' and (resid 363 through 466 )AD363 - 466284 - 387

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