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

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Basic information

Entry
Database: PDB / ID: 5ftc
TitleCrystal structure of Pif1 helicase from Bacteroides in complex with ADP
ComponentsTPR DOMAIN PROTEIN
KeywordsHYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE
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: 2.269 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2384
Polymers49,7311
Non-polymers5073
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.173, 74.032, 109.153
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: 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: 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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 0.1 CALCIUM ACETATE 10% PEG 4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.975
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.27→75.21 Å / Num. obs: 25850 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 50.21 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.56
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.82 / % possible all: 100

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Processing

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

5ftb


Resolution: 2.269→57.208 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1343 5.2 %
Rwork0.1945 --
obs0.1973 25843 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.269→57.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 29 75 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083579
X-RAY DIFFRACTIONf_angle_d0.8474841
X-RAY DIFFRACTIONf_dihedral_angle_d12.7382154
X-RAY DIFFRACTIONf_chiral_restr0.054545
X-RAY DIFFRACTIONf_plane_restr0.005613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2689-2.350.35211340.28382378X-RAY DIFFRACTION100
2.35-2.44410.28591280.24312427X-RAY DIFFRACTION100
2.4441-2.55540.32541490.23732405X-RAY DIFFRACTION100
2.5554-2.69010.33361360.24492422X-RAY DIFFRACTION100
2.6901-2.85860.32991420.25262411X-RAY DIFFRACTION100
2.8586-3.07930.34711270.25122429X-RAY DIFFRACTION100
3.0793-3.38920.35241030.2392482X-RAY DIFFRACTION100
3.3892-3.87950.24061440.19692458X-RAY DIFFRACTION100
3.8795-4.88730.20011350.14822477X-RAY DIFFRACTION100
4.8873-57.22620.18461450.15862611X-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)
14.07810.09020.30054.82120.24471.1170.04850.16580.30920.4361-0.02920.288-0.565-0.2235-0.02770.47750.05390.06030.4119-0.1060.3555-35.70865.27316.989
22.52480.72571.2843.20991.02742.6560.12140.8156-0.6262-0.0375-0.0261-0.12050.2483-0.2237-0.04340.36950.00010.02090.6995-0.25070.4623-37.8095-11.531411.5758
34.3221.1367-1.92372.3424-0.88995.5355-0.1187-0.288-0.2581-0.04520.0176-0.5256-0.06821.04140.130.4755-0.0144-0.0050.5681-0.21680.5626-9.8145-9.659525.1823
46.46390.09980.50641.25130.51572.69270.1035-0.62980.1550.2457-0.0624-0.033-0.1182-0.1128-0.01360.449-0.02550.00190.4561-0.03950.3455-25.8457-7.241435.9612
57.9371-1.08423.03011.11130.59297.0040.30340.9919-0.6028-0.14640.1624-0.1004-0.32550.6485-0.48780.4667-0.05520.09980.5302-0.13970.4423-15.1295-6.56379.7175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 55 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 56 THROUGH 191 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 192 THROUGH 262 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 263 THROUGH 370 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 371 THROUGH 431 )

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