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- PDB-3zdp: R416A Monomeric nucleoprotein of influenza A virus -

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Basic information

Entry
Database: PDB / ID: 3zdp
TitleR416A Monomeric nucleoprotein of influenza A virus
ComponentsNUCLEOCAPSID PROTEINVirus
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
: / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsChenavas, S. / Ruigrok, R.W.H. / Crepin, T.
CitationJournal: Plos Pathog. / Year: 2013
Title: Monomeric Nucleoprotein of Influenza a Virus.
Authors: Chenavas, S. / Estrozi, L.F. / Slama-Schwok, A. / Delmas, B. / Di Primo, C. / Baudin, F. / Li, X. / Crepin, T. / Ruigrok, R.W.
History
DepositionNov 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_label_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,2236
Polymers169,1063
Non-polymers1173
Water1,08160
1
A: NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4082
Polymers56,3691
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4082
Polymers56,3691
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4082
Polymers56,3691
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.420, 285.440, 118.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein NUCLEOCAPSID PROTEIN / Virus / NUCLEOPROTEIN


Mass: 56368.676 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/WSN/33 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1K9H2, UniProt: P15682*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 4.13 Å3/Da / Density % sol: 70.21 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 1.2 M POTASSIUM SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.69→10 Å / Num. obs: 77425 / % possible obs: 99.4 % / Observed criterion σ(I): 1.9 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.75
Reflection shellResolution: 2.69→2.82 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.91 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IQH

2iqh


Resolution: 2.69→143.12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.403 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24983 3889 5 %RANDOM
Rwork0.19779 ---
obs0.20039 73505 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.708 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--2.7 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.69→143.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11050 0 3 60 11113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911243
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.95115124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.88751383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88222.433563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.656152024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.85815147
X-RAY DIFFRACTIONr_chiral_restr0.120.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218605
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 290 -
Rwork0.336 5144 -
obs--99.78 %

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