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- PDB-4chc: Crystal structure of the N-terminal domain of the PA subunit of T... -

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Basic information

Entry
Database: PDB / ID: 4chc
TitleCrystal structure of the N-terminal domain of the PA subunit of Thogoto virus polymerase (form 2)
ComponentsPOLYMERASE ACIDIC PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


virion component / viral RNA genome replication / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase acidic protein
Similarity search - Component
Biological speciesTHOGOTO VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsGuilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
CitationJournal: Plos One / Year: 2014
Title: Comparative Structural and Functional Analysis of Orthomyxovirus Polymerase CAP-Snatching Domains.
Authors: Guilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
History
DepositionDec 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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 / struct_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYMERASE ACIDIC PROTEIN
B: POLYMERASE ACIDIC PROTEIN
C: POLYMERASE ACIDIC PROTEIN
D: POLYMERASE ACIDIC PROTEIN
E: POLYMERASE ACIDIC PROTEIN
F: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)123,0206
Polymers123,0206
Non-polymers00
Water00
1
E: POLYMERASE ACIDIC PROTEIN
F: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0072
Polymers41,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-11.1 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: POLYMERASE ACIDIC PROTEIN
D: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0072
Polymers41,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-10.1 kcal/mol
Surface area16580 Å2
MethodPISA
3
A: POLYMERASE ACIDIC PROTEIN
B: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0072
Polymers41,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10.2 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.000, 79.160, 70.300
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
POLYMERASE ACIDIC PROTEIN / RNA-DIRECTED RNA POLYMERASE SUBUNIT P3


Mass: 20503.381 Da / Num. of mol.: 6 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THOGOTO VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS-RIL / References: UniProt: P27194
Has protein modificationY
Nonpolymer detailsSELENOMETHIONINE (MSE): SELENOMETHIONATED PROTEIN
Sequence detailsEXTRA GMGSGMA AT N-TERMINUS AFTER HIS-TAG CLEAVAGE

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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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MGCL2, 0.1 M MES PH 6.5 AND 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 26711 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 51.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DHORI VIRUS POLYMERASE PA N-TERMINAL DOMAIN

Resolution: 2.77→102.18 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 40.504 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27868 1354 5.1 %RANDOM
Rwork0.2287 ---
obs0.23127 25357 92.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.75 Å2
2---0.35 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.77→102.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 0 0 7451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197615
X-RAY DIFFRACTIONr_bond_other_d0.0010.026957
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9310358
X-RAY DIFFRACTIONr_angle_other_deg0.668315999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45124.489401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.745151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1281551
X-RAY DIFFRACTIONr_chiral_restr0.0540.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021788
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_it0.662.133641
X-RAY DIFFRACTIONr_mcbond_other0.662.133640
X-RAY DIFFRACTIONr_mcangle_it1.2233.1874525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5342.1793974
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: 2.77→2.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 52 -
Rwork0.324 852 -
obs--42.38 %
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)
11.9483-0.5996-0.2915.71342.08822.7027-0.0164-0.20740.03230.00150.00030.1251-0.0019-0.10.01610.0045-0.0063-0.0160.04440.03210.1999-56.2459-11.12729.6464
23.69650.40040.20412.9678-1.83975.72220.01410.23920.24520.0346-0.12460.11280.04130.15490.11050.04310.0188-0.02090.06450.00190.2978-45.0299-12.021-0.0818
32.1210.6273-0.11025.5728-1.95543.34180.03610.3289-0.0993-0.1514-0.0702-0.12130.10270.15430.03410.02660.04-0.00870.12910.01120.2373-15.9776-9.274316.714
44.26930.88430.8232.98962.58046.30160.1311-0.35130.33330.1227-0.2506-0.12050.0176-0.10860.11960.0628-0.0266-0.02470.10060.03670.3246-26.8535-10.682546.4709
52.871.3561-0.40425.6425-1.39063.3274-0.05940.31740.1135-0.12890.00550.067-0.09490.06540.05380.05940.0272-0.02090.0667-0.02210.2581-82.3718-9.7185-6.6413
64.84661.48260.34182.98281.65136.910.1891-0.78410.36960.3145-0.49130.0608-0.0191-0.19340.30220.1835-0.055-0.00990.2808-0.06750.4552-93.1797-10.472823.6734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 165
2X-RAY DIFFRACTION2B2 - 166
3X-RAY DIFFRACTION3C3 - 165
4X-RAY DIFFRACTION4D2 - 166
5X-RAY DIFFRACTION5E3 - 165
6X-RAY DIFFRACTION6F2 - 166

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