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- PDB-4chd: Crystal structure of the '627' domain of the PB2 subunit of Thogo... -

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Basic information

Entry
Database: PDB / ID: 4chd
TitleCrystal structure of the '627' domain of the PB2 subunit of Thogoto virus polymerase
ComponentsPOLYMERASE ACIDIC PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


cap snatching / 7-methylguanosine mRNA capping / virion component / host cell nucleus
Similarity search - Function
Alpha-Beta Plaits - #3510 / : / : / Polymerase basic protein 2 (PB2), '627' domain / Polymerase basic protein 2, cap-binding domain / : / Influenza RNA polymerase PB2 helical domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesTHOGOTO VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: POLYMERASE ACIDIC PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,3051
Polymers18,3051
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.480, 65.480, 74.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18304.828 Da / Num. of mol.: 1 / Fragment: CENTRAL '627' DOMAIN, RESIDUES 543-701
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: Q9YNA4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA GAM 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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: SOLVED WITH SINGLE SITE MERCURY DERIVATIVE
Crystal growpH: 7
Details: THE PROTEIN WAS CONCENTRATED TO 2.3 MG/ML IN 250 MM NACL, 50 MM TRIS PH 8.0 AND 2 MM DTT AND CRYSTALS WERE GROWN IN 0.1 M HEPES PH 7.0, 0.2 M AMMONIUM SULPHATE AND 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6604 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.95 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→49.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.159 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23904 316 4.8 %RANDOM
Rwork0.20738 ---
obs0.20891 6288 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.362 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2---1.29 Å20 Å2
3---2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 0 17 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191090
X-RAY DIFFRACTIONr_bond_other_d0.0010.021075
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9661468
X-RAY DIFFRACTIONr_angle_other_deg0.69732476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3845134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65223.46949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1941511
X-RAY DIFFRACTIONr_chiral_restr0.060.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 24 -
Rwork0.308 455 -
obs--98.97 %
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)
14.45-3.1279-0.943311.2047-1.36767.2048-0.2106-0.1068-0.26970.2335-0.0746-0.58280.0160.70650.28520.0829-0.0465-0.00410.28370.02520.120118.009521.980814.162
29.2941-0.2299-1.97535.12070.12014.4701-0.1288-0.51470.18270.31240.0016-0.072-0.38570.00910.12710.19120.0188-0.00840.1690.04320.03687.514723.720419.5117
314.877-1.80051.7357.0585-2.4548.4513-0.0757-0.9868-0.80540.60670.057-0.42760.69490.6310.01870.28670.12060.03970.32720.11020.256815.514710.599623.0517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A547 - 581
2X-RAY DIFFRACTION2A582 - 644
3X-RAY DIFFRACTION3A645 - 681

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