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- PDB-5z6w: Crystal structure of paFAN1 bound to 2nt 5'flap DNA with gap with... -

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Basic information

Entry
Database: PDB / ID: 5z6w
TitleCrystal structure of paFAN1 bound to 2nt 5'flap DNA with gap with Manganese
Components
  • DNA (5'-D(P*AP*TP*TP*CP*AP*A)-3')
  • DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
  • Fanconi-associated nuclease 1 homolog
KeywordsHYDROLASE/DNA / Nuclease / Hydrolase-DNA complex
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / 5'-3' exonuclease activity / phosphodiesterase I activity / interstrand cross-link repair / manganese ion binding / magnesium ion binding
Similarity search - Function
Fanconi-associated nuclease 1, SAP domain / Fanconi anemia-associated nuclease SAP domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain / VRR_NUC / tRNA endonuclease-like domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Fanconi-associated nuclease 1 homolog
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJin, H. / Cho, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease.
Authors: Jin, H. / Roy, U. / Lee, G. / Scharer, O.D. / Cho, Y.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fanconi-associated nuclease 1 homolog
H: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
B: DNA (5'-D(P*AP*TP*TP*CP*AP*A)-3')
C: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3696
Polymers81,2594
Non-polymers1102
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-38 kcal/mol
Surface area33550 Å2
Unit cell
Length a, b, c (Å)80.874, 104.969, 105.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fanconi-associated nuclease 1 homolog / pFAN1


Mass: 66913.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: fan1, PA1865 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2N0, phosphodiesterase I

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DNA chain , 3 types, 3 molecules HBC

#2: DNA chain DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')


Mass: 3131.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*CP*AP*A)-3')


Mass: 3894.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')


Mass: 7319.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES(pH7.2), 25%(w/v) PEG 8000, 30mM Gly-gly-gly

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15512 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.981 / Rpim(I) all: 0.042 / Rsym value: 0.098 / Net I/σ(I): 16.19
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.981 / Num. unique obs: 762 / CC1/2: 0.651 / Rpim(I) all: 0.414 / Rsym value: 0.981

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1069: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R8A

4r8a


Resolution: 3.2→46.99 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2376 749 4.88 %
Rwork0.1823 --
obs0.185 15341 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 779 2 1 5226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135437
X-RAY DIFFRACTIONf_angle_d1.1557512
X-RAY DIFFRACTIONf_dihedral_angle_d22.0773101
X-RAY DIFFRACTIONf_chiral_restr0.053786
X-RAY DIFFRACTIONf_plane_restr0.007861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.4470.31471400.26712868X-RAY DIFFRACTION100
3.447-3.79380.30291420.22692887X-RAY DIFFRACTION100
3.7938-4.34240.26431530.18942881X-RAY DIFFRACTION100
4.3424-5.46970.21911470.17092919X-RAY DIFFRACTION100
5.4697-46.99490.19891670.15373037X-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)
11.951.0391-0.15242.45720.03682.09410.21060.28030.0413-0.01120.0614-0.6336-0.02920.36291.22760.5040.00680.09140.5821-0.02970.592437.3083-24.1351-28.8644
20.3835-0.71130.37171.30280.53320.1394-0.1594-0.11550.02520.08950.208-0.1269-0.05030.119400.55250.05420.11730.52490.09960.417413.1034-5.0725-27.6686
30.26160.65480.18480.31090.6028-0.0349-0.0401-0.2179-0.29550.4284-0.19160.3587-0.0627-0.1822-0.00050.8921-0.0560.21010.68050.02390.7212-12.4667-7.3017-10.6337
43.65260.8517-1.5321.6615-0.80811.80240.36540.68260.53670.1433-0.0280.315-0.126-0.41060.0010.4291-0.02180.01260.4215-0.03590.4828-10.219-21.7485-29.8879
51.6307-1.0338-2.39490.44091.45883.0621.79840.0417-0.1855-0.0750.7962-0.52170.105-1.53641.03270.7954-0.4132-0.42260.9960.16830.702824.1667-36.7592-18.207
60.0736-0.08070.02430.0384-0.05980.0393-0.1654-0.4224-1.0627-0.0822-1.1454-0.25220.16210.9723-0.0011.994-0.02420.00012.1995-0.12162.0513-1.1179-11.7485-2.7118
70.45990.05730.24220.05380.03560.41910.1555-0.14010.2394-0.50270.1170.4389-0.54890.0217-0.16581.275-0.1111-0.14161.81550.24872.37571.2709-7.7835-7.6851
80.00830.0134-0.0162-0.0176-0.01410.016-0.591-0.5898-0.05790.03550.1008-0.6115-0.35680.408-0.00132.69090.38370.20162.56550.2772.22289.6322-19.083-23.1106
91.28680.1207-0.1890.0846-0.06790.11570.28860.5201-1.29521.66570.87470.84361.0532-0.94810.18441.2577-0.0618-0.06640.930.01810.694924.9105-38.0649-15.1939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 168 )
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 366 )
4X-RAY DIFFRACTION4chain 'A' and (resid 367 through 559 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 10 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 14 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'C' and (resid 8 through 12 )
9X-RAY DIFFRACTION9chain 'C' and (resid 13 through 24 )

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