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- PDB-4aqf: X-ray crystallographic structure of Crimean-congo haemorrhagic fe... -

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Basic information

Entry
Database: PDB / ID: 4aqf
TitleX-ray crystallographic structure of Crimean-congo haemorrhagic fever virus nucleoprotein
Components(NUCLEOPROTEIN) x 2
KeywordsVIRAL PROTEIN / NAIROVIRUS
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds / hydrolase activity / ribonucleoprotein complex / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1110 / Nucleocapsid N protein / Nucleocapsid N protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsWang, Y. / Dutta, S. / Karlberg, H. / Devignot, S. / Weber, F. / Hao, Q. / Tan, Y.J. / Mirazimi, A. / Kotaka, M.
CitationJournal: J.Virol. / Year: 2012
Title: Structure of Crimean-Congo Haemorraghic Fever Virus Nucleoprotein: Superhelical Homo-Oligomers and the Role of Caspase-3 Cleavage.
Authors: Wang, Y. / Dutta, S. / Karlberg, H. / Devignot, S. / Weber, F. / Hao, Q. / Tan, Y.J. / Mirazimi, A. / Kotaka, M.
History
DepositionApr 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: NUCLEOPROTEIN
B: NUCLEOPROTEIN
C: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4927
Polymers162,1083
Non-polymers3844
Water5,206289
1
A: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2233
Polymers54,0311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2233
Polymers54,0311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NUCLEOPROTEIN


Theoretical massNumber of molelcules
Total (without water)54,0451
Polymers54,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.119, 133.119, 289.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-1477-

SO4

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.702, 0.665, 0.256), (-0.713, 0.656, 0.248), (-0.003, -0.356, 0.934)33.789, 80.711, -58.668
2given(0.787, -0.564, 0.249), (0.583, 0.812, -0.005), (-0.2, 0.149, 0.968)42.765, -79.137, 40.832

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Components

#1: Protein NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 54031.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P89522
#2: Protein NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N


Mass: 54045.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Plasmid: PGEX-6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): RIL / References: UniProt: P89522
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 4.55 Å3/Da / Density % sol: 72.96 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M MES, PH 6.5, 37% (V/V) PEG 200, 12% (V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 54514 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.1→29.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 35.36 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23328 2769 5.1 %RANDOM
Rwork0.17013 ---
obs0.17332 51772 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 20 289 11397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211335
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.94815302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38551401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67524.99515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.998152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5441548
X-RAY DIFFRACTIONr_chiral_restr0.0890.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218492
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_restr7.72511335
X-RAY DIFFRACTIONr_sphericity_free27.5135231
X-RAY DIFFRACTIONr_sphericity_bonded31.07711166
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 197 -
Rwork0.298 3465 -
obs--100 %
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)
11.2248-0.12490.3580.0223-0.07670.28470.0585-0.01390.20610.0401-0.01050.0055-0.21810-0.0480.40330.04710.06980.0954-0.01010.188267.5132-46.9113.1238
22.3545-0.54511.05450.2875-0.20480.5013-0.0876-0.1679-0.15560.02610.14230.0635-0.0693-0.0782-0.05470.06370.0088-0.02260.30590.09210.0471114.4933-82.527834.2048
30.2472-0.04270.33921.175-0.18231.17590.04390.0349-0.0220.15030.1476-0.19570.07430.2596-0.19150.06920.0537-0.01070.1217-0.03040.247945.79516.5213-30.5187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 482
2X-RAY DIFFRACTION2B1 - 482
3X-RAY DIFFRACTION3C1 - 482

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