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- PDB-3upu: Crystal structure of the T4 Phage SF1B Helicase Dda -

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Basic information

Entry
Database: PDB / ID: 3upu
TitleCrystal structure of the T4 Phage SF1B Helicase Dda
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • ATP-dependent DNA helicase dda
KeywordsHYDROLASE/DNA / RecA-like domain / SH3 domain / pin-tower interface / coupling ATP hydrolysis to DNA unwinding / ssDNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA helicase activity / helicase activity / DNA helicase / DNA replication / ATP binding
Similarity search - Function
SH3 type barrels. - #780 / Dda helicase SH3 domain / Dda helicase SH3 domain / AAA domain / SH3 type barrels. / P-loop containing nucleotide triphosphate hydrolases / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase ...SH3 type barrels. - #780 / Dda helicase SH3 domain / Dda helicase SH3 domain / AAA domain / SH3 type barrels. / P-loop containing nucleotide triphosphate hydrolases / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / ATP-dependent DNA helicase dda
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.299 Å
AuthorsHe, X. / Yun, M.K. / Pemble IV, C.W. / Kreuzer, K.N. / Raney, K.D. / White, S.W.
CitationJournal: Structure / Year: 2012
Title: The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation.
Authors: He, X. / Byrd, A.K. / Yun, M.K. / Pemble, C.W. / Harrison, D. / Yeruva, L. / Dahl, C. / Kreuzer, K.N. / Raney, K.D. / White, S.W.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase dda
B: ATP-dependent DNA helicase dda
C: ATP-dependent DNA helicase dda
D: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
E: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
F: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)164,6536
Polymers164,6536
Non-polymers00
Water18010
1
A: ATP-dependent DNA helicase dda
D: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,8842
Polymers54,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-21 kcal/mol
Surface area22400 Å2
MethodPISA
2
B: ATP-dependent DNA helicase dda
E: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,8842
Polymers54,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-17 kcal/mol
Surface area22680 Å2
MethodPISA
3
C: ATP-dependent DNA helicase dda
F: 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)54,8842
Polymers54,8842
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-20 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.536, 107.253, 85.475
Angle α, β, γ (deg.)90.000, 94.128, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ATP-dependent DNA helicase dda / SF1B Helicase Dda


Mass: 52495.719 Da / Num. of mol.: 3 / Mutation: K38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: dda, sud / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P32270, DNA helicase
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2388.585 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CORRESPONDS TO NCBI AAA32488.1.

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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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4.5% w/v PEG8000, 8% v/v ethylene glycol, 0.1 M HEPES, pH 6.5, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.1K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
177.21
277.21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9793
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJun 19, 2009
MARMOSAIC 225 mm CCD2CCDOct 29, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal Si(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
211
ReflectionResolution: 3.299→36.035 Å / Num. obs: 29389 / % possible obs: 95.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 92.36 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.82
Reflection shellResolution: 3.299→3.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.05 / % possible all: 71.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
SERGUIControldata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.299→32.271 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7879 / SU ML: 0.4 / σ(F): 0 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1392 4.99 %RANDOM
Rwork0.2038 ---
obs0.2065 29389 91.06 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.539 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 313.71 Å2 / Biso mean: 110.0717 Å2 / Biso min: 32.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.8054 Å20 Å2-7.0719 Å2
2--19.6229 Å20 Å2
3----20.4283 Å2
Refinement stepCycle: LAST / Resolution: 3.299→32.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10566 471 0 10 11047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411331
X-RAY DIFFRACTIONf_angle_d0.91615428
X-RAY DIFFRACTIONf_chiral_restr0.0611732
X-RAY DIFFRACTIONf_plane_restr0.0041871
X-RAY DIFFRACTIONf_dihedral_angle_d18.4494216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.299-3.41640.4098870.33171634172157
3.4164-3.5530.30341310.30142243237478
3.553-3.71450.321230.26292664278791
3.7145-3.910.32881580.23912732289094
3.91-4.15450.29871380.22152769290796
4.1545-4.47450.26991560.19162873302998
4.4745-4.92340.20721500.1662865301599
4.9234-5.63250.25431460.1962916306299
5.6325-7.0840.27331470.198229273074100
7.084-32.27230.21610.176129703131100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.52760.3608-0.34151.9256-0.47442.4023-0.0279-0.31940.00780.1570.0113-0.0473-0.12620.0631-0.00340.2591-0.02140.03970.5246-0.0650.290110.8557-20.8365-19.4984
21.31510.59580.11613.0374-0.80281.30180.2294-0.17330.2263-0.0542-0.27350.4192-0.2307-0.02250.00060.61930.00860.04680.4846-0.10080.633745.72025.0842-47.5557
32.28390.41380.29441.06070.09631.4268-0.3266-0.01050.046-0.01310.01850.29930.25950.0457-0.00220.6525-0.13030.01130.39960.06830.578361.863319.9728-8.5176
40.0685-0.05660.00010.22090.1440.1138-0.20970.1471-0.0884-0.20330.18-0.41420.30.2197-0.00070.7077-0.0109-0.04871.33660.11860.834518.7312-22.0122-22.943
50.25210.04870.13570.01180.02520.07330.0036-0.37750.1071-0.76540.22590.72580.1896-0.63550.01151.31690.00860.17320.8677-0.14851.214541.772-1.5197-51.0284
60.1953-0.0271-0.05290.12040.03130.01920.5598-0.50560.60120.9538-0.23070.2606-0.3180.1148-0.00141.4256-0.1504-0.12271.11390.17741.1566.013127.0974-6.8138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 439
2X-RAY DIFFRACTION2chain BB1 - 439
3X-RAY DIFFRACTION3chain CC1 - 439
4X-RAY DIFFRACTION4chain DD600 - 607
5X-RAY DIFFRACTION5chain EE600 - 607
6X-RAY DIFFRACTION6chain FF600 - 607

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