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- PDB-2ic9: The Coiled-coil Domain (residues 1-93) Structure of the Sin Nombr... -

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Basic information

Entry
Database: PDB / ID: 2ic9
TitleThe Coiled-coil Domain (residues 1-93) Structure of the Sin Nombre Virus Nucleocapsid Protein
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / Sin Nombre Virus / Hantavirus / Bunyaviridae / ssRNA negative-strand viruses / nucleocapsid protein / antiparallel coiled coil
Function / homology
Function and homology information


regulation of translation / viral nucleocapsid / endonuclease activity / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesSin Nombre virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoudko, S.P. / Rossmann, M.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Coiled-coil Domain Structure of the Sin Nombre Virus Nucleocapsid Protein.
Authors: Boudko, S.P. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)21,4002
Polymers21,4002
Non-polymers00
Water1,65792
1
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)10,7001
Polymers10,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)10,7001
Polymers10,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.774, 42.647, 57.996
Angle α, β, γ (deg.)90.000, 121.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleocapsid protein


Mass: 10700.089 Da / Num. of mol.: 2 / Fragment: Residues: 1-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sin Nombre virus / Genus: Hantavirus / Strain: Convict Creek 107 virus / Gene: nucleocapsid protein / Plasmid: pET23d(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81930, UniProt: Q89462*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M potassium bromide, 0.1 M Tris-HCl, 34% PEG mono-methyl ether (PEG MME) 200, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2006 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 12283 / Num. obs: 12165 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Χ2: 1.079 / Net I/σ(I): 32.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1194 / Rsym value: 0.248 / Χ2: 1.181 / % possible all: 99

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Phasing

Phasing MRRfactor: 0.517 / Cor.coef. Fo:Fc: 0.38
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IC6, chain A

2ic6


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.869 / SU B: 6.892 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1235 10.2 %RANDOM
Rwork0.247 ---
all0.257 12263 --
obs0.257 12141 98.8 %-
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: 43.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.24 Å2
2---0.84 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 0 92 1226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221136
X-RAY DIFFRACTIONr_angle_refined_deg2.44421526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.10725.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33715238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.991512
X-RAY DIFFRACTIONr_chiral_restr0.1820.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02808
X-RAY DIFFRACTIONr_nbd_refined0.2820.2589
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.210
X-RAY DIFFRACTIONr_mcbond_it1.5541.5760
X-RAY DIFFRACTIONr_mcangle_it2.35721158
X-RAY DIFFRACTIONr_scbond_it3.9833424
X-RAY DIFFRACTIONr_scangle_it5.8394.5368
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 85 -
Rwork0.302 786 -
obs-871 98.75 %

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