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- PDB-8f5m: Crystal structure of P74 gp62 -

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Basic information

Entry
Database: PDB / ID: 8f5m
TitleCrystal structure of P74 gp62
ComponentsEnvelope glycoprotein gp62
KeywordsREPLICATION / Polymerase / thermophage
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesThermus virus P74-26
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBae, B. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.
Authors: Chaban, A. / Minakhin, L. / Goldobina, E. / Bae, B. / Hao, Y. / Borukhov, S. / Putzeys, L. / Boon, M. / Kabinger, F. / Lavigne, R. / Makarova, K.S. / Koonin, E.V. / Nair, S.K. / Tagami, S. / ...Authors: Chaban, A. / Minakhin, L. / Goldobina, E. / Bae, B. / Hao, Y. / Borukhov, S. / Putzeys, L. / Boon, M. / Kabinger, F. / Lavigne, R. / Makarova, K.S. / Koonin, E.V. / Nair, S.K. / Tagami, S. / Severinov, K. / Sokolova, M.L.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp62
B: Envelope glycoprotein gp62
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3254
Polymers137,2762
Non-polymers492
Water14,970831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-28 kcal/mol
Surface area52350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.937, 210.102, 181.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Envelope glycoprotein gp62


Mass: 68638.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus virus P74-26 / Gene: P74p62 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXN5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: 20-30 % PEG 3350, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98756 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98756 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 84905 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.7
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 1.295 / Num. unique obs: 4103 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
REFMACrefmac5refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.406 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23146 3937 5 %RANDOM
Rwork0.18611 ---
obs0.18836 74282 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å20 Å2
2---0.08 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 2 831 10150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129579
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.63813044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29651181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37421.289512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.759151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1491576
X-RAY DIFFRACTIONr_chiral_restr0.1110.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027430
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_it3.1674.0564730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9796.0735909
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7614.3114848
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.00254.52714643
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
Rfree0.315 223 -
Rwork0.267 4081 -
obs--71.29 %

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