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- PDB-2q06: Crystal structure of Influenza A Virus H5N1 Nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 2q06
TitleCrystal structure of Influenza A Virus H5N1 Nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN / Influenza / H5N1 / Nucleoprotein
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNg, A.K.L. / Zhang, H. / Tan, K. / Wang, J. / Shaw, P.C.
CitationJournal: Faseb J. / Year: 2008
Title: Structure of the influenza virus A H5N1 nucleoprotein: implications for RNA binding, oligomerization, and vaccine design.
Authors: Ng, A.K. / Zhang, H. / Tan, K. / Li, Z. / Liu, J.H. / Chan, P.K. / Li, S.M. / Chan, W.Y. / Au, S.W. / Joachimiak, A. / Walz, T. / Wang, J.H. / Shaw, P.C.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)113,6872
Polymers113,6872
Non-polymers00
Water00
1
A: Nucleoprotein

A: Nucleoprotein

A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)170,5303
Polymers170,5303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area14260 Å2
ΔGint-54 kcal/mol
Surface area59270 Å2
MethodPISA, PQS
2
B: Nucleoprotein

B: Nucleoprotein

B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)170,5303
Polymers170,5303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area14130 Å2
ΔGint-54 kcal/mol
Surface area61570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.578, 153.578, 153.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Nucleoprotein


Mass: 56843.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: H5N1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9PX50

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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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.15 M KCl, 0.01 M MgCl2, 0.1 M cacodylate pH 6.2, 7% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97845 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 3.3→48.564 Å / Num. all: 18405 / Num. obs: 18405 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 90.08 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.16
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1192 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IQH

2iqh


Resolution: 3.3→46.32 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.868 / SU B: 67.078 / SU ML: 0.495 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.609 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 945 5.1 %RANDOM
Rwork0.202 ---
all0.206 18405 --
obs0.206 18379 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.109 Å2
Refinement stepCycle: LAST / Resolution: 3.3→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 0 0 0 7343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227460
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.94710027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44522.347375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.203151345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66915104
X-RAY DIFFRACTIONr_chiral_restr0.0840.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025720
X-RAY DIFFRACTIONr_nbd_refined0.280.33900
X-RAY DIFFRACTIONr_nbtor_refined0.3360.55197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.5490
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.3250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.533
X-RAY DIFFRACTIONr_mcbond_it0.4321.54673
X-RAY DIFFRACTIONr_mcangle_it0.7827380
X-RAY DIFFRACTIONr_scbond_it0.87233049
X-RAY DIFFRACTIONr_scangle_it1.5744.52647
LS refinement shellResolution: 3.301→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 63 -
Rwork0.244 1251 -
obs-1314 99.1 %
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)
11.65151.51420.14668.92470.09062.7186-0.289-0.3960.17190.41450.43-0.2535-0.1765-0.5132-0.1409-0.22940.30570.02640.0958-0.1923-0.401711.259-2.429-21.004
21.4496-0.81070.62551.3736-0.35041.35-0.2394-0.3456-0.07710.20870.1990.0548-0.2042-0.24360.0404-0.29360.14310.0268-0.0662-0.0854-0.26565.194-0.894-36.021
30.87490.2963-2.69252.3621-2.80779.8754-0.0276-0.0838-0.1764-0.0345-0.0702-0.12280.15370.50180.0978-0.08150.03090.0793-0.283-0.0582-0.1282.1718.936-78.619
44.9628-1.13511.53552.3907-0.76491.6131-0.1020.5948-0.0902-0.4120.0099-0.0852-0.02080.42460.0921-0.28260.11160.1206-0.1852-0.0372-0.338914.134-1.526-55.307
53.6362-0.4345-0.10533.4514-0.25525.4863-0.278-0.44480.6965-0.16340.1115-0.2774-0.68460.30610.1665-0.1381-0.0933-0.0889-0.2284-0.2355-0.265247.0662.205-6.276
61.253-0.58550.08711.9251.06112.3022-0.0424-0.17330.2964-0.0358-0.0927-0.1551-0.1834-0.18390.1351-0.2708-0.0431-0.028-0.1964-0.0926-0.287442.925-10.775-15.218
72.26470.712.204713.30842.12432.30320.1848-0.4321-0.23650.524-0.3553-0.49450.1595-0.41570.1705-0.2624-0.03680.0785-0.270.0711-0.152647.038-53.854-35.548
82.1532-0.24370.37643.47062.75.02850.2813-0.244-0.44030.6797-0.11860.10320.7093-0.4628-0.1627-0.1708-0.06110.0306-0.26210.0674-0.426140.936-31.621-11.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 78
2X-RAY DIFFRACTION2A87 - 395
3X-RAY DIFFRACTION3A396 - 435
4X-RAY DIFFRACTION4A436 - 496
5X-RAY DIFFRACTION5B21 - 77
6X-RAY DIFFRACTION6B88 - 395
7X-RAY DIFFRACTION7B396 - 435
8X-RAY DIFFRACTION8B436 - 495

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