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- PDB-5fhh: Structure of human Pif1 helicase domain residues 200-641 -

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Basic information

Entry
Database: PDB / ID: 5fhh
TitleStructure of human Pif1 helicase domain residues 200-641
ComponentsATP-dependent DNA helicase PIF1
KeywordsHYDROLASE / Pif1 helicase / SF1B 5'-3' DNA helicase
Function / homology
Function and homology information


5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / : / regulation of telomere maintenance / DNA duplex unwinding / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase ...5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / : / regulation of telomere maintenance / DNA duplex unwinding / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / replication fork / 5'-3' DNA helicase activity / DNA recombination / DNA replication / DNA helicase / chromosome, telomeric region / DNA repair / magnesium ion binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
Helicase / : / : / DNA helicase Pif1, 2B domain / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.6 Å
AuthorsZhou, X. / Ren, W. / Bharath, S.R. / Song, H.
CitationJournal: Cell Rep / Year: 2016
Title: Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1
Authors: Zhou, X. / Ren, W. / Bharath, S.R. / Tang, X. / He, Y. / Chen, C. / Liu, Z. / Li, D. / Song, H.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
B: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0736
Polymers96,0122
Non-polymers1,0604
Water00
1
A: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5363
Polymers48,0061
Non-polymers5302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-4 kcal/mol
Surface area16910 Å2
MethodPISA
2
B: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5363
Polymers48,0061
Non-polymers5302
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint2 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.750, 204.750, 77.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1


Mass: 48006.152 Da / Num. of mol.: 2 / Fragment: UNP residues 200-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIF1, C15orf20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H611, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3% tacsimate, 0.1M Bis-Tris, 15% glycerol, 15% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→71.2 Å / Num. obs: 22636 / % possible obs: 94.9 % / Redundancy: 5.9 % / Net I/σ(I): 8.3
Reflection shellResolution: 3.5→3.78 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.3 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.6→47.062 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3548 1043 5.04 %
Rwork0.3103 --
obs0.3125 20701 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→47.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 64 0 5128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075309
X-RAY DIFFRACTIONf_angle_d1.3557308
X-RAY DIFFRACTIONf_dihedral_angle_d13.0583074
X-RAY DIFFRACTIONf_chiral_restr0.06909
X-RAY DIFFRACTIONf_plane_restr0.008947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5996-3.78930.40051220.31862386X-RAY DIFFRACTION80
3.7893-4.02660.36431540.32512430X-RAY DIFFRACTION83
4.0266-4.33730.38961620.30162935X-RAY DIFFRACTION99
4.3373-4.77340.33351190.30242980X-RAY DIFFRACTION100
4.7734-5.46320.37211650.32562951X-RAY DIFFRACTION99
5.4632-6.87970.36491620.33542951X-RAY DIFFRACTION99
6.8797-47.06650.31531590.29083025X-RAY DIFFRACTION98
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)
14.15-2.2609-1.58456.84220.44092.05810.21090.39780.3433-0.1129-0.1344-1.2128-0.35680.0936-0.25790.3765-0.0257-0.06130.27160.03370.4649-92.984444.6384-8.6628
25.216-0.3071-0.51324.28840.36032.6017-0.2577-0.3073-1.056-0.29090.63650.14540.65160.1350.10720.56950.1118-0.07120.3971-0.00680.8101-87.494129.59380.7164
33.99840.67-0.36242.11350.23540.5954-0.7978-0.30980.51520.25820.25980.20590.0230.11970.36810.40180.0475-0.06210.37660.02310.6609-99.112943.03563.5524
42.0715-0.73780.22192.0164-0.75092.8924-0.08570.6295-0.56530.5177-0.19610.28320.2594-0.82550.36990.6350.0068-0.10730.5566-0.16231.8805-116.445921.4133-7.1305
53.92880.47430.82332.82990.84844.53310.46360.438-1.014-0.8069-0.32470.7528-1.3124-0.01070.0390.69960.08260.01830.61530.01221.1428-105.762522.546-11.0981
63.73880.4497-0.47223.84811.82823.1802-0.58710.8894-0.4964-1.23280.20310.0372-0.3660.09910.09760.8419-0.0318-0.27120.84-0.78371.2829-111.573823.2776-21.6478
75.1836-0.48072.15823.17060.71451.15270.1856-0.24620.08470.6785-0.26320.81761.13040.03710.46180.60890.02640.17820.5053-0.00320.485-95.119919.2627-9.5114
82.72111.00240.51162.1102-0.13131.27350.36620.0813-0.8620.00180.15450.37520.46690.0280.0880.3255-0.2755-0.32960.35240.03041.6073-113.987133.7493-0.5838
93.63871.9712-1.26683.0021-0.91550.90190.258-0.7404-0.32590.57-0.78620.3175-0.2556-0.08660.11350.4580.224-0.06050.35520.04161.0017-112.973844.24455.3187
101.23960.4646-0.28752.06930.19172.2037-0.32190.08510.0926-0.55840.28730.6398-0.8230.3564-0.1080.7510.0270.10570.3357-0.09751.0558-73.731732.1844-30.4818
112.82450.6328-0.9323.3018-0.48061.51640.07650.24-0.12190.4822-0.513-1.02290.30630.00410.29530.9237-0.163-0.23310.296-0.29392.0123-83.903914.6171-26.4462
121.98450.6661-1.30322.0287-1.69642.6254-0.02350.68520.1121-0.69620.55620.02970.6295-0.484-0.37531.1683-0.2001-0.13530.5027-0.37621.9423-85.409121.0675-32.3
131.4087-0.8357-1.0457.6535-0.79311.0390.5929-0.3394-0.0572-2.12950.02132.3130.3731-0.8047-0.31070.9896-0.0084-0.15421.0374-0.33991.6708-76.154919.1925-41.095
141.2614-0.1423-0.98842.3881-2.23753.2829-0.1511-0.5232-0.5372-0.7320.2413-1.25660.68261.29640.17850.91960.01580.35891.0778-0.55922.8471-51.893519.1533-29.5285
156.87110.7074-0.13850.1135-0.21662.1276-1.0474-0.44960.4385-0.0930.715-2.1950.321.16080.47780.92360.25530.07810.92160.0642.629-67.60297.1166-8.2473
162.9108-1.77040.27821.7056-0.23651.7172-0.4944-0.226-0.81870.15760.8943-1.0271-0.52030.8512-0.39360.57480.1984-0.06710.3654-0.29562.2778-66.523717.9621-11.5148
170.0498-0.1820.05133.4995-1.91131.37950.3546-0.04380.0046-0.39080.2599-0.7108-0.00621.0077-0.82471.13950.11040.26891.0014-0.57922.2033-54.311513.5773-28.6425
182.0270.3466-0.6732.67121.17530.96340.69870.1463-1.044-1.250.1909-0.50130.38890.2107-0.4061.4203-0.12450.55331.0663-0.54623.0115-59.161914.0974-41.0219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 205:256 )A205 - 256
2X-RAY DIFFRACTION2( CHAIN A AND RESID 257:312 )A257 - 312
3X-RAY DIFFRACTION3( CHAIN A AND RESID 313:410 )A313 - 410
4X-RAY DIFFRACTION4( CHAIN A AND RESID 411:458 )A411 - 458
5X-RAY DIFFRACTION5( CHAIN A AND RESID 459:494 )A459 - 494
6X-RAY DIFFRACTION6( CHAIN A AND RESID 495:527 )A495 - 527
7X-RAY DIFFRACTION7( CHAIN A AND RESID 528:547 )A528 - 547
8X-RAY DIFFRACTION8( CHAIN A AND RESID 548:584 )A548 - 584
9X-RAY DIFFRACTION9( CHAIN A AND RESID 585:615 )A585 - 615
10X-RAY DIFFRACTION10( CHAIN B AND RESID 205:256 )B205 - 256
11X-RAY DIFFRACTION11( CHAIN B AND RESID 257:288 )B257 - 288
12X-RAY DIFFRACTION12( CHAIN B AND RESID 289:345 )B289 - 345
13X-RAY DIFFRACTION13( CHAIN B AND RESID 346:374 )B346 - 374
14X-RAY DIFFRACTION14( CHAIN B AND RESID 375:428 )B375 - 428
15X-RAY DIFFRACTION15( CHAIN B AND RESID 429:479 )B429 - 479
16X-RAY DIFFRACTION16( CHAIN B AND RESID 480:567 )B480 - 567
17X-RAY DIFFRACTION17( CHAIN B AND RESID 568:593 )B568 - 593
18X-RAY DIFFRACTION18( CHAIN B AND RESID 594:615 )B594 - 615

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