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

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Basic information

Entry
Database: PDB / ID: 5oea
TitleStructure of large terminase from the thermophilic bacteriophage D6E in complex with ATP-gamma-S (Crystal form 3)
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 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Large subunit terminase
Function and homology information
Biological speciesDeep-sea thermophilic phage D6E (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

Downloads & links

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Assembly

Deposited unit
A: Large subunit terminase
B: Large subunit terminase
C: Large subunit terminase
D: Large subunit terminase
E: Large subunit terminase
F: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,32314
Polymers294,1336
Non-polymers2,1908
Water2,378132
1
A: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5703
Polymers49,0221
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5703
Polymers49,0221
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5703
Polymers49,0221
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Large subunit terminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5703
Polymers49,0221
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Large subunit terminase


Theoretical massNumber of molelcules
Total (without water)49,0221
Polymers49,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.476, 102.981, 103.044
Angle α, β, γ (deg.)90.980, 119.370, 117.180
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Large subunit terminase


Mass: 49022.129 Da / Num. of mol.: 6
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-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M Ammonium Sulafte, 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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→45.9 Å / Num. obs: 59382 / % possible obs: 96.5 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.071 / Rrim(I) all: 0.104 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.0820.8110.3790.7751.12396.5
13.42-45.91.90.0230.9980.0220.03292.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.9 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 24.354 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.462
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 3165 5.3 %RANDOM
Rwork0.1895 ---
obs0.1928 56215 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.15 Å2 / Biso mean: 79.046 Å2 / Biso min: 33.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20.13 Å2-1.06 Å2
2--4 Å20.13 Å2
3----1.29 Å2
Refinement stepCycle: final / Resolution: 3→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19345 0 110 132 19587
Biso mean--94.28 62.46 -
Num. residues----2428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01919987
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217746
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.93827072
X-RAY DIFFRACTIONr_angle_other_deg0.8642.99840938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36652421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.623.955943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.036153236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7231590
X-RAY DIFFRACTIONr_chiral_restr0.0640.22859
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024424
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 281 -
Rwork0.35 4086 -
all-4367 -
obs--96.55 %

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