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- PDB-5ftf: Crystal structure of Pif1 helicase from Bacteroides double mutant... -

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Basic information

Entry
Database: PDB / ID: 5ftf
TitleCrystal structure of Pif1 helicase from Bacteroides double mutant L95C-I339C
ComponentsTPR DOMAIN PROTEIN
KeywordsHYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE / DISULPHIDE BRIDGE
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TPR domain protein
Similarity search - Component
Biological speciesBACTEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.412 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 13, 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 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1382
Polymers49,7111
Non-polymers4271
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.708, 73.482, 108.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TPR DOMAIN PROTEIN / HELICASE


Mass: 49710.938 Da / Num. of mol.: 1 / Mutation: YES
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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M BIS-TRIS PROPANE PH 6.5 0.1M CALCIUM ACETATE 10% PEG 4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979142
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979142 Å / Relative weight: 1
ReflectionResolution: 2.41→60.87 Å / Num. obs: 19410 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 52.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.15
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.57 / % possible all: 97

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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: 2.412→60.868 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2999 1003 5.2 %
Rwork0.2127 --
obs0.2172 19387 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.412→60.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 27 30 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143576
X-RAY DIFFRACTIONf_angle_d1.3464837
X-RAY DIFFRACTIONf_dihedral_angle_d15.9342155
X-RAY DIFFRACTIONf_chiral_restr0.065543
X-RAY DIFFRACTIONf_plane_restr0.01613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4123-2.53950.35441420.27172793X-RAY DIFFRACTION98
2.5395-2.69860.39581090.27921990X-RAY DIFFRACTION69
2.6986-2.9070.33691620.26912860X-RAY DIFFRACTION100
2.907-3.19950.40581610.27132895X-RAY DIFFRACTION100
3.1995-3.66240.34731360.24942346X-RAY DIFFRACTION83
3.6624-4.6140.29771210.19142505X-RAY DIFFRACTION88
4.614-60.88720.22631720.16582995X-RAY DIFFRACTION98

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