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- PDB-5a97: Hazara virus nucleocapsid protain -

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Basic information

Entry
Database: PDB / ID: 5a97
TitleHazara virus nucleocapsid protain
ComponentsNUCLEOCAPSID PROTEIN
KeywordsVIRAL PROTEIN / HAZARA / NUCLEOCAPSID
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
Nucleocapsid N protein / Nucleocapsid N protein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesHAZARA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSurtees, R. / Ariza, A. / Hewson, R. / Barr, J.N. / Edwards, T.A.
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: The Crystal Structure of the Hazara Virus Nucleocapsid Protein.
Authors: Surtees, R. / Ariza, A. / Punch, E.K. / Trinh, C.H. / Dowall, S.D. / Hewson, R. / Hiscox, J.A. / Barr, J.N. / Edwards, T.A.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
D: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)218,5694
Polymers218,5694
Non-polymers00
Water1,26170
1
A: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,6421
Polymers54,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,6421
Polymers54,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,6421
Polymers54,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,6421
Polymers54,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.989, 76.102, 449.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NUCLEOCAPSID PROTEIN


Mass: 54642.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAZARA VIRUS / Strain: JC280 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: M4PWE6, UniProt: P27318*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5
Details: 15% PEG 10,000, 0.1 M SODIUM CITRATE PH 5, 0.1 M NACL, 2 % DIOXANE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97779
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 2.6→65.25 Å / Num. obs: 74079 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.1
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AKL

4akl


Resolution: 2.7→224.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 22.904 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28217 3125 5.1 %RANDOM
Rwork0.24182 ---
obs0.24384 58670 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→224.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15023 0 0 70 15093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915484
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214849
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.95220919
X-RAY DIFFRACTIONr_angle_other_deg0.876334284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54651927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76824.905687
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.822152806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.261569
X-RAY DIFFRACTIONr_chiral_restr0.0590.22269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023501
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_it1.7216.9117687
X-RAY DIFFRACTIONr_mcbond_other1.7216.9117686
X-RAY DIFFRACTIONr_mcangle_it3.03610.3599609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3476.9557797
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 203 -
Rwork0.37 4181 -
obs--97.23 %
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)
13.4876-0.81612.93144.674-1.97527.3426-0.1702-0.27380.4920.52420.57720.3245-0.7456-1.3569-0.4070.57640.3046-0.1410.82430.21110.5432-19.319634.7048-112.366
21.3891-0.0602-0.10021.1861-0.40562.1404-0.0047-0.02270.27650.0135-0.0395-0.1413-0.16970.15010.04420.1218-0.0756-0.1010.10890.01790.184212.488949.0104-169.2032
32.69230.52110.27142.9339-0.52651.48330.1795-0.0146-0.22390.1907-0.0985-0.37440.04890.0742-0.0810.0259-0.0044-0.02180.00590.00160.1914-31.234534.4745-225.3059
41.157-0.42541.21333.4765-0.60042.5170.2003-0.013-0.0527-0.263-0.1047-0.14660.2992-0.0287-0.09560.0742-0.0557-0.00280.17330.05860.1243-13.15085.1159-167.6133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 185
2X-RAY DIFFRACTION1A198 - 486
3X-RAY DIFFRACTION2B0 - 186
4X-RAY DIFFRACTION2B196 - 485
5X-RAY DIFFRACTION3C-3 - 186
6X-RAY DIFFRACTION3C197 - 485
7X-RAY DIFFRACTION4D0 - 186
8X-RAY DIFFRACTION4D196 - 485

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