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- PDB-5fte: Crystal structure of Pif1 helicase from Bacteroides in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5fte
TitleCrystal structure of Pif1 helicase from Bacteroides in complex with ADP-AlF3 and ssDNA
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP)-3'
  • TPR DOMAIN PROTEIN
KeywordsHYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA repair / nucleotide binding / metal ion binding
Similarity search - Function
DNA helicase Pif1-like / PIF1-like helicase / UvrD-like helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / DNA / TPR domain protein
Similarity search - Component
Biological speciesBACTEROIDES (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsChen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, M. / Dou, S.-X. / Li, N. / Dong, Y.-H. / Rety, S. / Xi, X.-G.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Crystal Structures of the Bspif1 Helicase Reveal that a Major Movement of the 2B SH3 Domain is Required for DNA Unwinding
Authors: Chen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, N. / Li, M. / Dou, S.-X. / Dong, Y.-H. / Rety, S. / Xi, X.-G.
History
DepositionJan 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPR DOMAIN PROTEIN
D: 5'-D(*TP*TP*TP*TP*TP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0475
Polymers51,5112
Non-polymers5353
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-31 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.743, 86.743, 149.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TPR DOMAIN PROTEIN / HELICASE


Mass: 49730.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES (bacteria) / Strain: SP. 3_1_23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7K0H3, DNA helicase
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP)-3'


Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Sequence detailsNCBI REFERENCE SEQUENCE WP_008647876.1

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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: 3.27 Å3/Da / Density % sol: 62.4 % / Description: NONE
Crystal growpH: 7.1
Details: 0.1M HEPES PH 7.1 3.5M SODIUM FORMATE 5% GLYCEROL 0.01M SPERMIDINE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.19→75.12 Å / Num. obs: 11303 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 107.86 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.62
Reflection shellResolution: 3.19→3.3 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.59 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FTB

5ftb


Resolution: 3.19→75.122 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 568 5 %
Rwork0.2212 --
obs0.2241 11302 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→75.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 120 32 0 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033696
X-RAY DIFFRACTIONf_angle_d0.7325022
X-RAY DIFFRACTIONf_dihedral_angle_d16.3252198
X-RAY DIFFRACTIONf_chiral_restr0.046567
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1897-3.51070.41121240.3362625X-RAY DIFFRACTION100
3.5107-4.01870.36691480.26462645X-RAY DIFFRACTION100
4.0187-5.0630.28291480.20412670X-RAY DIFFRACTION100
5.063-75.14240.22591480.19522794X-RAY DIFFRACTION100
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)
14.55060.1469-1.35552.20760.79997.17240.1209-0.3603-0.30420.06460.1034-0.25120.31860.4597-0.18530.809-0.0243-0.08840.5604-0.00690.7432-27.407610.1546159.5224
26.546-0.9878-1.93663.2067-1.27652.8454-0.12120.86850.6361-0.37420.22260.0854-0.0962-0.2716-0.10171.0586-0.0888-0.02211.0398-0.18240.8783-29.217924.2284134.1747
34.9433-0.47610.29443.25251.38485.77760.16570.0422-0.029-0.1917-0.11770.17690.1094-0.8388-0.10371.1007-0.147-0.02940.77040.01090.8575-52.272519.8456145.3893
44.04991.20241.13460.98142.4555.7656-0.21280.0917-0.3675-0.2007-0.1113-0.00630.0643-0.91740.22910.87020.030.00220.49370.14250.7294-44.164521.0444152.2178
53.72230.9199-1.67052.3129-1.984.0593-0.550.1971-0.20440.22540.0921-0.6322-0.38930.84430.47920.9205-0.0844-0.03120.7881-0.17391.0648-17.815519.3154148.461
66.21.9482-3.32265.6833-4.49439.23890.0224-0.6976-0.01011.0601-0.0011-0.0679-1.3408-0.5285-0.12251.02960.08620.06211.21440.05890.9735-38.408523.312156.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 202 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 203 THROUGH 247 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 248 THROUGH 314 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 315 THROUGH 382 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 383 THROUGH 431 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 3 THROUGH 8 )

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