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- PDB-5y7g: Crystal structure of paFAN1 bound to 1nt 5'flap DNA with gap -

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Basic information

Entry
Database: PDB / ID: 5y7g
TitleCrystal structure of paFAN1 bound to 1nt 5'flap DNA with gap
Components
  • DNA (5'-D(P*GP*AP*AP*TP*GP*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')
  • DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-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: 3.4 Å
AuthorsCho, Y. / Jin, H.
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
DepositionAug 17, 2017Deposition 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 ...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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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
B: Fanconi-associated nuclease 1 homolog
C: Fanconi-associated nuclease 1 homolog
D: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
E: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
G: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
H: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
I: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
J: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
L: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
N: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,99117
Polymers244,79112
Non-polymers2005
Water00
1
A: Fanconi-associated nuclease 1 homolog
D: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
E: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
J: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6776
Polymers81,5974
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-76 kcal/mol
Surface area33830 Å2
MethodPISA
2
B: Fanconi-associated nuclease 1 homolog
F: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
G: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
L: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6776
Polymers81,5974
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-71 kcal/mol
Surface area34730 Å2
MethodPISA
3
C: Fanconi-associated nuclease 1 homolog
H: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
I: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*AP*CP*TP*T)-3')
N: DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6375
Polymers81,5974
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-58 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.290, 143.258, 172.712
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 Fanconi-associated nuclease 1 homolog / pFAN1


Mass: 66913.266 Da / Num. of mol.: 3
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
#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.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*AP*AP*TP*GP*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.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*CP*AP*A)-3')


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca

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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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M Bis-Tris-Propane (pH7.6), 12%(w/v) PEG 8000, 0.2M Sodium acetate trihydrate, 10mM Calcium chloride dihydrate, 1%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 46805 / % possible obs: 96.6 % / Redundancy: 12 % / Rmerge(I) obs: 0.162 / Rsym value: 0.162 / Net I/σ(I): 26.9
Reflection shellRmerge(I) obs: 1.913 / CC1/2: 0.222 / Rpim(I) all: 0.575 / Rsym value: 1.913

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Processing

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

4r8a


Resolution: 3.4→33.58 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.99
RfactorNum. reflection% reflection
Rfree0.2798 2368 5.11 %
Rwork0.221 --
obs0.2241 46339 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13231 2928 5 0 16164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316868
X-RAY DIFFRACTIONf_angle_d1.42623421
X-RAY DIFFRACTIONf_dihedral_angle_d21.7929532
X-RAY DIFFRACTIONf_chiral_restr0.0722458
X-RAY DIFFRACTIONf_plane_restr0.0092592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.46940.45691240.3922437X-RAY DIFFRACTION92
3.4694-3.54480.39241240.37512427X-RAY DIFFRACTION92
3.5448-3.62710.42711400.34922483X-RAY DIFFRACTION92
3.6271-3.71770.38891520.32822467X-RAY DIFFRACTION94
3.7177-3.81810.37261330.3182517X-RAY DIFFRACTION94
3.8181-3.93030.42771270.3112547X-RAY DIFFRACTION94
3.9303-4.05690.34591370.29112499X-RAY DIFFRACTION94
4.0569-4.20170.37431530.29372547X-RAY DIFFRACTION94
4.2017-4.36960.35941530.27342555X-RAY DIFFRACTION95
4.3696-4.5680.32951450.24942587X-RAY DIFFRACTION97
4.568-4.80810.32431140.24872628X-RAY DIFFRACTION97
4.8081-5.10840.32481430.23612649X-RAY DIFFRACTION98
5.1084-5.50130.35111410.23452676X-RAY DIFFRACTION98
5.5013-6.0520.3511430.22772700X-RAY DIFFRACTION99
6.052-6.9210.32111300.22642743X-RAY DIFFRACTION99
6.921-8.69470.22771490.18742752X-RAY DIFFRACTION99
8.6947-33.58170.17651600.14082757X-RAY DIFFRACTION96
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)
12.73452.0819-0.87354.4034-4.02562.3071-0.0998-0.1920.55111.17120.50681.4354-0.6968-0.1867-0.211.68510.34430.60761.0071-0.01361.6333-20.666521.692755.3947
23.0554-0.019-0.9995.99571.68973.79550.0756-0.0774-0.07460.63240.44170.32770.1478-0.0826-0.38621.20680.07750.00660.80110.27050.8919-10.1456-14.82949.7365
32.15364.12682.45843.85091.19713.88750.0559-1.2480.71460.6434-0.06370.48670.4441-1.4862-0.01051.026-0.1710.38351.9522-0.1271.5353-21.1352-30.0976110.27
43.3038-0.4863-1.3132.20280.25742.08960.42950.6160.51220.0154-0.7493-0.13640.0940.03370.27191.0540.2002-0.20321.42890.21351.487514.657-29.791297.1572
53.7672-1.3312.27552.7970.73752.57780.1053-0.7301-0.3190.3604-0.31060.65710.5544-1.1269-0.02511.6368-0.4880.07121.65180.23741.057815.285311.5908106.6906
62.27732.3372-2.18296.893-2.77951.3320.0716-0.5367-1.2304-1.1857-0.4311-0.10591.2340.08210.53012.24950.28860.07561.6587-0.16161.648432.30884.220169.4333
78.67840.5418-3.3367.3461.90685.50210.1313-0.57560.264-0.17340.0226-0.46220.2246-0.47580.14061.59990.2083-0.56251.20170.251.320725.431329.946974.5637
85.85324.0342-4.39916.4379-4.70045.1457-0.13742.76170.6642-1.47622.03982.84240.8205-1.8352-1.8051.65830.0450.09692.4140.38141.9078-23.232914.387236.2408
95.2217-2.43484.07917.116-4.33894.4913-0.22680.5511-0.4929-1.65531.9421.32320.7212-0.0934-0.90251.8339-0.4177-0.00761.846-0.19871.49591.2311-7.67136.2248
102.6335-0.387-1.0750.18690.31310.6565-0.29262.3-0.75230.0584-0.0940.46850.49380.93560.75682.0111-0.16050.40392.06420.23613.0835-26.43632.000340.4161
114.83314.8604-4.19115.105-4.49588.28380.20251.85420.3399-1.13141.0441.25211.4435-1.5383-1.52061.9343-0.266-0.11911.93420.04291.9012-19.903319.350430.4879
126.4428-0.44971.23896.90833.99368.47671.2209-0.9635-1.47630.62830.1591-2.56051.7439-2.0653-1.20271.9054-0.487-0.26152.0676-0.05831.9458-12.5944-49.1813108.9391
132.01262.5456-5.73289.2042-4.08244.5545-0.0368-1.2846-4.2432-1.6967-2.7231-1.06722.68490.06850.89181.75170.1374-0.15433.46450.50352.1638.655-40.292882.1013
140.61890.0578-0.35460.9883-0.06220.1860.29841.508-0.3786-1.3242-0.0029-2.04980.861-0.137-0.65351.8663-0.55190.26321.8243-0.26142.2093-1.1912-42.8426111.5525
153.88751.23363.5650.35751.06763.55520.9205-1.3551-1.80911.2321-0.7813-0.28722.252-0.0368-0.63692.2547-0.2066-0.69141.56020.40781.7391-17.0128-54.8064105.1112
161.5059-0.4758-2.02913.66391.41193.7388-1.5050.12010.53911.29411.0561-0.8277-0.19441.4141-0.1172.45350.2988-1.11592.39040.05642.898434.406322.6979109.9985
178.53751.83591.45091.32281.08353.8879-1.05610.2099-0.9635-2.5513-0.7972-1.6549-0.60881.13681.07513.1133-0.0164-0.07121.6551-0.15982.28538.83058.281781.8701
183.91210.3086-2.99660.80240.9564.74820.0612-0.874-1.54850.55820.88790.2489-0.81510.512-0.83522.43020.1629-0.69352.18180.33442.457236.392622.6082108.2763
198.7177-0.2247-3.43612.8042-0.84148.1009-0.4996-0.86513.85830.5950.9855-1.1905-0.04591.1854-1.22861.75890.10170.20931.7427-0.19541.78981.1083-7.914237.85
208.59446.5887-1.75416.6148-3.23542.44120.54840.5115-1.71710.301-1.1652-0.2481.3322-2.70850.56221.84950.4994-0.06572.9454-0.28331.92199.4559-40.629881.9318
212.6662-1.49210.46423.12183.48019.0696-1.56560.3743-0.33360.97810.2474-1.42631.23991.14710.6012.13790.33450.12382.05470.22982.298338.30997.605580.821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 556 )
3X-RAY DIFFRACTION3chain 'B' and (resid 17 through 195 )
4X-RAY DIFFRACTION4chain 'B' and (resid 196 through 559 )
5X-RAY DIFFRACTION5chain 'C' and (resid 18 through 289 )
6X-RAY DIFFRACTION6chain 'C' and (resid 290 through 366 )
7X-RAY DIFFRACTION7chain 'C' and (resid 367 through 558 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 10 )
10X-RAY DIFFRACTION10chain 'E' and (resid 11 through 15 )
11X-RAY DIFFRACTION11chain 'E' and (resid 16 through 24 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 10 )
13X-RAY DIFFRACTION13chain 'G' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'G' and (resid 11 through 15 )
15X-RAY DIFFRACTION15chain 'G' and (resid 16 through 24 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 10 )
17X-RAY DIFFRACTION17chain 'I' and (resid 1 through 10 )
18X-RAY DIFFRACTION18chain 'I' and (resid 11 through 24 )
19X-RAY DIFFRACTION19chain 'J' and (resid 1 through 14 )
20X-RAY DIFFRACTION20chain 'L' and (resid 1 through 14 )
21X-RAY DIFFRACTION21chain 'N' and (resid 2 through 14 )

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