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

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Basic information

Entry
Database: PDB / ID: 4cgx
TitleCrystal structure of the N-terminal domain of the PA subunit of Thogoto virus polymerase (form 1)
ComponentsPOLYMERASE ACIDIC PROTEIN
KeywordsTRANSCRIPTION
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: 2.7 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
DepositionNov 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE ACIDIC PROTEIN
B: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,0072
Polymers41,0072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-11.5 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.930, 77.230, 67.750
Angle α, β, γ (deg.)90.00, 123.27, 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.: 2 / 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
Sequence detailsEXTRA GMGSG AT N-TERMINAL 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: 2.32 Å3/Da / Density % sol: 47 % / 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: BM14 / Wavelength: 0.9786
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 9879 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 56.29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CGS

4cgs


Resolution: 2.7→41.815 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 471 4.8 %
Rwork0.1997 --
obs0.2035 9876 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→41.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 0 0 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032659
X-RAY DIFFRACTIONf_angle_d0.8223615
X-RAY DIFFRACTIONf_dihedral_angle_d13.902965
X-RAY DIFFRACTIONf_chiral_restr0.036401
X-RAY DIFFRACTIONf_plane_restr0.003461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-3.09070.34821630.25993091X-RAY DIFFRACTION98
3.0907-3.89350.32791480.21133128X-RAY DIFFRACTION99
3.8935-41.82020.23681600.17793186X-RAY DIFFRACTION99
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)
14.1366-0.8421.50281.8998-2.31134.4135-0.39040.4243-0.67580.0009-0.38590.06281.66520.6137-0.01670.99790.13850.33260.43710.0550.82753.5039-38.345213.4232
20.6888-0.23850.87092.91220.59623.4-0.6251-0.448-0.4817-0.564-0.4778-0.12731.28481.21270.16540.61460.20140.1810.60690.21570.56851.2807-32.523720.0672
34.2392-2.29131.73934.3914-0.292.8414-0.0137-0.02730.5939-0.1799-0.231-0.0782-0.32890.01590.24820.5707-0.06640.00220.30470.01310.4469-7.1037-19.87913.7154
45.661-0.9493-1.31585.3120.23345.4691.2266-0.19530.8318-1.1269-1.317-1.0084-0.0750.33710.27590.6104-0.14250.1510.4640.12260.56012.664-15.308912.5743
52.8081-0.71511.433.6353-1.76785.7743-0.3617-0.38420.06920.5937-0.1435-0.5073-1.65511.6580.25340.5605-0.2238-0.00120.78660.03720.6023.4861-18.48325.2108
64.6967-2.27430.20472.34932.22915.8443-0.1703-1.3578-0.00320.50060.518-0.61960.13621.66610.89490.48310.0398-0.13751.10890.15830.53254.2377-25.476831.0567
72.6560.14520.11649.00070.4032.20920.0168-0.59150.4040.37980.1726-0.0048-0.53471.03820.34760.8464-0.1226-0.18270.66930.05020.4336-2.4307-19.379133.2573
83.9535-3.5139-0.87637.46492.95951.7541-1.0395-0.4447-1.02090.6506-0.04430.20751.59490.52960.68290.86730.12590.37860.62610.24470.6741-1.0076-36.426230.2566
92.3858-0.0918-0.32229.4945-1.68971.7259-0.4216-0.7092-1.22730.1466-0.4199-1.47720.87572.12890.27630.58810.26120.05591.3150.38250.719814.0291-39.580925.8633
103.25361.249-1.32216.8033-0.62920.4833-0.52360.86520.4157-1.10070.30850.1696-0.2612-0.41320.16850.65960.0356-0.11950.63690.00690.4585-21.2947-19.5673-1.2141
113.48421.19270.19672.51461.32373.83650.0012-0.0918-0.59140.216-0.39820.22090.3363-0.52840.24120.3480.0233-0.03810.4068-0.02540.4474-26.0489-31.71819.5162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 47 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 48 THROUGH 74 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 75 THROUGH 86 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 87 THROUGH 114 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 115 THROUGH 126 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 127 THROUGH 134 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 135 THROUGH 154 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 155 THROUGH 165 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 2 THROUGH 100 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 101 THROUGH 166 )

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