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- PDB-8h2m: gp96 RNA polymerase from P23-45 phage (crystal 1) -

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Basic information

Entry
Database: PDB / ID: 8h2m
Titlegp96 RNA polymerase from P23-45 phage (crystal 1)
ComponentsTape tail measure protein
KeywordsTRANSCRIPTION / RNA polymerase
Function / homology: / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / PUA domain profile. / metalloendopeptidase activity / membrane / metal ion binding / Tape tail measure protein
Function and homology information
Biological speciesOshimavirus P2345
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.08 Å
AuthorsChaban, A. / Sokolova, M.L. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328, 22H01346 Japan
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
DepositionOct 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 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: Tape tail measure protein


Theoretical massNumber of molelcules
Total (without water)134,9941
Polymers134,9941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.780, 137.780, 135.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Tape tail measure protein


Mass: 134994.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GB YP_001467949.1 / Source: (gene. exp.) Oshimavirus P2345 / Gene: P23p96 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXD0
Has ligand of interestN
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1000, 100 mM Tris-HCl buffer (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.08→40.96 Å / Num. obs: 46152 / % possible obs: 100 % / Redundancy: 86.9 % / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 3.08→3.27 Å / Redundancy: 76.5 % / Num. unique obs: 7612 / CC1/2: 0.475 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.08→40.96 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 3745 8.12 %
Rwork0.2051 42355 -
obs0.2091 46100 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.2 Å2 / Biso mean: 79.0407 Å2 / Biso min: 32.84 Å2
Refinement stepCycle: final / Resolution: 3.08→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5933 0 0 0 5933
Num. residues----754
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.08-3.120.39381390.363715711710100
3.12-3.160.39741390.347615921731100
3.16-3.20.3381360.355315971733100
3.2-3.250.38391380.330815301668100
3.25-3.30.36371460.263815781724100
3.3-3.350.32261450.250215461691100
3.35-3.40.29911310.243715751706100
3.4-3.460.34471530.23415651718100
3.46-3.530.29451280.225915691697100
3.53-3.590.24371490.213615441693100
3.59-3.670.28631420.21415791721100
3.67-3.750.31231340.209615731707100
3.75-3.830.29621260.208715981724100
3.83-3.930.28311380.203815521690100
3.93-4.040.23771220.192715781700100
4.04-4.150.241470.177115671714100
4.15-4.290.23811360.168515711707100
4.29-4.440.21361380.156715601698100
4.44-4.620.18241330.145415861719100
4.62-4.830.21151400.157515571697100
4.83-5.080.22251470.146115581705100
5.08-5.40.19571480.173115651713100
5.4-5.820.24141350.187215601695100
5.82-6.40.22511510.225815621713100
6.4-7.320.28561340.227515761710100
7.32-9.20.20251430.20315701713100
9.21-40.960.26361270.22951576170399
Refinement TLS params.Method: refined / Origin x: 17.2542 Å / Origin y: 46.7669 Å / Origin z: 74.0599 Å
111213212223313233
T0.442 Å2-0.0966 Å20.0334 Å2-0.5925 Å2-0.0797 Å2--0.4879 Å2
L0.4951 °2-0.4143 °20.165 °2-2.6291 °2-0.9166 °2--0.9688 °2
S0.1131 Å °-0.1215 Å °0.1972 Å °0.0646 Å °-0.0316 Å °0.0726 Å °-0.192 Å °0.2492 Å °-0.0807 Å °
Refinement TLS groupSelection details: all

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