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- PDB-2ic6: The Coiled-coil Domain (residues 1-75) Structure of the Sin Nombr... -

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Basic information

Entry
Database: PDB / ID: 2ic6
TitleThe Coiled-coil Domain (residues 1-75) 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 / host cell Golgi apparatus / viral nucleocapsid / endonuclease activity / 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 / MAD / Resolution: 1.15 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 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,4182
Polymers17,4182
Non-polymers00
Water4,414245
1
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)8,7091
Polymers8,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)8,7091
Polymers8,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.116, 49.521, 100.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleocapsid protein


Mass: 8708.889 Da / Num. of mol.: 2 / Fragment: Residues: 1-75
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.: 245 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% polyethylene glycol (PEG) 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9002
SYNCHROTRONAPS 23-ID-D20.97964, 0.97948, 0.95373
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDOct 30, 2005Bent conical Si-mirror (Rh coating)
MARMOSAIC 300 mm CCD2CCDDec 15, 2005Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Bent cylindrical Ge(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) double drystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.90021
20.979641
30.979481
40.953731
Reflection

D res high: 1.33 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
7.4116.82136050.0761.082888985.8
7.2215.92097430.0711.012893385.8
7.4315.72214740.0721.052999988.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.875082.510.0631.1488.4
2.272.8791.110.0761.0598.4
1.992.279410.0841.0748.2
1.811.9995.510.1021.0868.1
1.681.8196.410.1061.0248.2
1.581.6897.110.1161.0917.7
1.51.5897.510.1291.0667.8
1.431.584.210.1591.0545.8
1.381.4366.510.1761.0775.1
1.331.3852.210.2041.0583.7
2.875083.620.0581.0228.5
2.272.8791.120.0721.0998.4
1.992.279420.081.0018.2
1.811.9995.420.0990.9998.1
1.681.8196.520.1080.9898.1
1.581.6897.120.1230.9747.6
1.51.5897.520.1370.9887.5
1.431.584.220.1740.9665.5
1.381.436620.1910.9654.6
1.331.3851.520.2230.9993
2.87508330.0581.0718.5
2.272.8790.730.0731.1518.5
1.992.2793.430.0771.018.3
1.811.999530.1021.0718.1
1.681.8196.230.111.0598.2
1.581.6896.930.1231.0027.6
1.51.5897.330.1340.9787.7
1.431.595.630.171.0256.5
1.381.4377.130.21.035.2
1.331.3862.230.2361.0313.6
ReflectionResolution: 1.15→10 Å / Num. all: 50803 / Num. obs: 50773 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 1.03 / Net I/σ(I): 27.4
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2516 / Rsym value: 0.238 / Χ2: 1.039 / % possible all: 99.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97954.33-10.03
13 wavelength20.97962.48-8.45
13 wavelength30.95372.84-3.38
Phasing MAD set siteAtom type symbol: Se / B iso: 12.405 / Fract x: 0.171 / Fract y: 0.09 / Fract z: 0.058 / Occupancy: 0.692
Phasing dmFOM : 0.78 / FOM acentric: 0.78 / FOM centric: 0.76 / Reflection: 29724 / Reflection acentric: 26983 / Reflection centric: 2741
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.8-19.7630.960.970.951274982292
2.4-3.80.950.950.9140633530533
1.9-2.40.90.90.8552984738560
1.7-1.90.820.830.754034900503
1.4-1.70.710.720.5895338803730
1.3-1.40.510.510.5241534030123

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.15→10 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.982 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2572 5.1 %RANDOM
Rwork0.154 ---
all0.156 50694 --
obs0.156 50689 99.86 %-
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: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--1.11 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 245 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221187
X-RAY DIFFRACTIONr_bond_other_d0.0020.02823
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9971598
X-RAY DIFFRACTIONr_angle_other_deg1.22132040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0965145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27925.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40915256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4521512
X-RAY DIFFRACTIONr_chiral_restr0.2220.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined0.2650.2303
X-RAY DIFFRACTIONr_nbd_other0.20.2890
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2595
X-RAY DIFFRACTIONr_nbtor_other0.0950.2663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.224
X-RAY DIFFRACTIONr_mcbond_it2.6581.5964
X-RAY DIFFRACTIONr_mcbond_other0.9731.5292
X-RAY DIFFRACTIONr_mcangle_it2.89221204
X-RAY DIFFRACTIONr_scbond_it4.6553478
X-RAY DIFFRACTIONr_scangle_it6.3784.5394
X-RAY DIFFRACTIONr_rigid_bond_restr2.34732305
X-RAY DIFFRACTIONr_sphericity_free11.2813245
X-RAY DIFFRACTIONr_sphericity_bonded5.68932007
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 159 -
Rwork0.152 3496 -
obs-3655 99.48 %

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