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- PDB-5oe9: Structure of large terminase from the thermophilic bacteriophage ... -

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Basic information

Entry
Database: PDB / ID: 5oe9
TitleStructure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (Crystal form 2)
ComponentsLarge subunit terminase
KeywordsVIRAL PROTEIN / large terminase
Function / homologyBacteriophage terminase, large subunit / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Large subunit terminase
Function and homology information
Biological speciesDeep-sea thermophilic phage D6E (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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

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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)150,9808
Polymers150,4993
Non-polymers4805
Water5,639313
1
A: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2632
Polymers50,1661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2632
Polymers50,1661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4554
Polymers50,1661
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)181.297, 102.249, 110.282
Angle α, β, γ (deg.)90.000, 124.870, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A13 - 417
2010B13 - 417
1020A13 - 417
2020C13 - 417
1030B13 - 420
2030C13 - 420

NCS ensembles :
ID
1
2
3

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M Ammonium Sulfate, 0.1 M HEPES pH 8.0 / 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: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.38→46.65 Å / Num. obs: 64217 / % possible obs: 97.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Net I/σ(I): 13.5 / Num. measured all: 268569 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.38-2.443.31.1310.420.6521.31367.4
10.91-46.654.10.020.9990.0110.02396.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.4→46.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.911 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.233
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 3007 4.7 %RANDOM
Rwork0.1949 ---
obs0.1967 60933 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.52 Å2 / Biso mean: 69.991 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å21.35 Å2
2---4.18 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 2.4→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9776 0 25 315 10116
Biso mean--94.62 62.27 -
Num. residues----1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910057
X-RAY DIFFRACTIONr_bond_other_d0.0010.028967
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.94113635
X-RAY DIFFRACTIONr_angle_other_deg0.943320692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52851228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1323.907471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.348151629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5131546
X-RAY DIFFRACTIONr_chiral_restr0.0780.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022229
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A248400.08
12B248400.08
21A250700.08
22C250700.08
31B253260.07
32C253260.07
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 155 -
Rwork0.339 4294 -
all-4449 -
obs--94.26 %

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