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- PDB-8h2n: gp96 RNA polymerase from P23-45 phage (crystal 2) -

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Basic information

Entry
Database: PDB / ID: 8h2n
Titlegp96 RNA polymerase from P23-45 phage (crystal 2)
ComponentsTape tail measure protein
KeywordsTRANSCRIPTION / RNA polymerase
Function / homology
Function and homology information


metalloendopeptidase activity / killing of cells of another organism / defense response to bacterium / metal ion binding / membrane
Similarity search - Function
: / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / PUA domain profile.
Similarity search - Domain/homology
Tape tail measure protein
Similarity search - Component
Biological speciesThermus virus P23-45
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.41 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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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 1.3Nov 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: Tape tail measure protein
B: Tape tail measure protein
C: Tape tail measure protein
D: Tape tail measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,2898
Polymers368,1924
Non-polymers974
Water00
1
A: Tape tail measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0722
Polymers92,0481
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tape tail measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0722
Polymers92,0481
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tape tail measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0722
Polymers92,0481
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tape tail measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0722
Polymers92,0481
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.158, 128.910, 136.758
Angle α, β, γ (deg.)90.000, 96.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tape tail measure protein


Mass: 92048.062 Da / Num. of mol.: 4 / Fragment: gp96 RNA polymerase fragment 327-1124
Source method: isolated from a genetically manipulated source
Details: GB YP_001467949.1 / Source: (gene. exp.) Thermus virus P23-45 / Gene: P23p96 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXD0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22.5% 2-Methyl-2,4-pentanediol, 12.5% PEG 3350, 100 mM HEPES (pH 7.5), 100 mM NH4OAc, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.41→44.37 Å / Num. obs: 50313 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.989 / Net I/σ(I): 4.08
Reflection shellResolution: 4.41→4.52 Å / Redundancy: 3.6 % / Num. unique obs: 3691 / CC1/2: 0.191 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H2M

8h2m


Resolution: 4.41→44.37 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3027 3868 7.71 %
Rwork0.2452 46279 -
obs0.2498 50147 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 329.83 Å2 / Biso mean: 203.2815 Å2 / Biso min: 125.72 Å2
Refinement stepCycle: final / Resolution: 4.41→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22380 0 4 0 22384
Biso mean--148.27 --
Num. residues----2836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.41-4.460.44531310.37531597172895
4.46-4.520.33711320.35211607173998
4.52-4.580.33051410.32571640178197
4.58-4.640.341360.31841629176598
4.64-4.710.34951450.32951687183299
4.71-4.780.38991350.334616081743100
4.78-4.850.38741400.32721677181799
4.85-4.930.3831380.33271653179199
4.93-5.020.37181400.320916491789100
5.02-5.110.35131390.32616661805100
5.11-5.210.34611400.333516481788100
5.21-5.310.33281390.322516761815100
5.31-5.430.37921400.322816591799100
5.43-5.550.38131360.312416471783100
5.55-5.690.41821380.337216861824100
5.69-5.840.38411420.321716791821100
5.84-6.020.361350.313216451780100
6.02-6.210.34331390.299616941833100
6.21-6.430.3471360.288316371773100
6.43-6.690.3631340.280816481782100
6.69-6.990.37641440.267117131857100
6.99-7.360.30271350.260616311766100
7.36-7.820.31321390.227116551794100
7.82-8.420.26691430.195616931836100
8.42-9.260.23511360.177816461782100
9.26-10.580.21851420.155716681810100
10.58-13.270.23141360.16181645178199
13.27-44.370.25621370.18571596173396
Refinement TLS params.Method: refined / Origin x: 78.4404 Å / Origin y: -53.5385 Å / Origin z: 51.0859 Å
111213212223313233
T1.4482 Å2-0.0217 Å2-0.0154 Å2-1.4162 Å20.0953 Å2--1.3744 Å2
L0.0057 °20.0362 °20.0408 °2--0.0346 °20.0029 °2--0.0689 °2
S-0.0158 Å °0.1145 Å °0.1435 Å °-0.0711 Å °0.038 Å °-0.0526 Å °0.0565 Å °0.1159 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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