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- PDB-5oe8: Structure of large terminase from the thermophilic bacteriophage ... -

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Basic information

Entry
Database: PDB / ID: 5oe8
TitleStructure of large terminase from the thermophilic bacteriophage D6E (Crystal form 2)
ComponentsLarge subunit terminase
KeywordsVIRAL PROTEIN / large terminase
Function / homologyBacteriophage terminase, large subunit / Terminase large subunit, T4likevirus-type, N-terminal / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / Large subunit terminase
Function and homology information
Biological speciesDeep-sea thermophilic phage D6E (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, R.G. / Jenkins, H.T. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust101528 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis.
Authors: Xu, R.G. / Jenkins, H.T. / Antson, A.A. / Greive, S.J.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large subunit terminase
B: Large subunit terminase
C: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,7129
Polymers150,4993
Non-polymers2136
Water13,854769
1
A: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2373
Polymers50,1661
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2373
Polymers50,1661
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2373
Polymers50,1661
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.085, 101.584, 108.500
Angle α, β, γ (deg.)90.000, 124.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-848-

HOH

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Components

#1: Protein Large subunit terminase


Mass: 50166.492 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deep-sea thermophilic phage D6E (virus)
Production host: Escherichia coli (E. coli) / References: UniProt: E5DV50
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Ammonium Sulfate, 0.1 M HEPES pH 6.5-8.5. / PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→46.05 Å / Num. obs: 80788 / % possible obs: 99.5 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Rrim(I) all: 0.091 / Net I/σ(I): 11.6 / Num. measured all: 335994 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.243.91.0651705143720.4790.6011.2271.494.6
11.22-46.053.50.0421206130.9960.0240.04636.593.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.362 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 3787 4.7 %RANDOM
Rwork0.1862 ---
obs0.1886 77001 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.98 Å2 / Biso mean: 50.295 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.16 Å2
2---1.98 Å20 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 2.2→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9803 0 6 770 10579
Biso mean--51.6 50.63 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910058
X-RAY DIFFRACTIONr_bond_other_d0.0020.029000
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.93913620
X-RAY DIFFRACTIONr_angle_other_deg0.909320809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84224.037488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78151670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1411548
X-RAY DIFFRACTIONr_chiral_restr0.0740.21433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022226
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 297 -
Rwork0.305 5412 -
all-5709 -
obs--95.58 %

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