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- PDB-4r8a: Crystal structure of paFAN1 - 5' flap DNA complex -

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Basic information

Entry
Database: PDB / ID: 4r8a
TitleCrystal structure of paFAN1 - 5' flap DNA complex
Components
  • DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*A)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
  • Uncharacterized protein
KeywordsHydrolase/DNA / DNA binding / metal binding nuclease / 5'flap DNA endo nuclease / fanconi anemia proteins family / Hydrolase-DNA complex
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsCho, Y. / Gwon, G.H. / Kim, Y.R.
CitationJournal: Genes Dev. / Year: 2014
Title: Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1
Authors: Gwon, G.H. / Kim, Y.R. / Liu, Y. / Watson, A.T. / Jo, A. / Etheridge, T.J. / Yuan, F. / Zhang, Y. / Kim, Y.C. / Carr, A.M. / Cho, Y.
History
DepositionAug 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
B: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')
C: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
D: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*A)-3')
F: Uncharacterized protein
G: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-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*A)-3')


Theoretical massNumber of molelcules
Total (without water)157,3428
Polymers157,3428
Non-polymers00
Water362
1
A: Uncharacterized protein
B: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')
C: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
D: DNA (5'-D(P*GP*AP*AP*TP*GP*TP*GP*TP*GP*TP*CP*TP*CP*AP*AP*TP*CP*CP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)78,6714
Polymers78,6714
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-33 kcal/mol
Surface area33200 Å2
MethodPISA
2
F: Uncharacterized protein
G: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-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*A)-3')


Theoretical massNumber of molelcules
Total (without water)78,6714
Polymers78,6714
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-33 kcal/mol
Surface area33220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.581, 106.663, 142.180
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 16:553 )
211CHAIN F AND (RESSEQ 16:553 )
112CHAIN D AND (RESSEQ 1:21 )
212CHAIN I AND (RESSEQ 1:21 )
113CHAIN B AND (RESSEQ -2:12 )
213CHAIN G AND (RESSEQ -2:12 )
114CHAIN C AND (RESSEQ 1:10 )
214CHAIN H AND (RESSEQ 1:10 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Uncharacterized protein / Nuclease


Mass: 64610.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1865 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2N0
#2: DNA chain DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')


Mass: 4506.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')


Mass: 3131.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
#4: 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*A)-3')


Mass: 6422.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Dec 23, 2013
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.17→50 Å / Num. obs: 45784 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 99.12 Å2
Reflection shellHighest resolution: 3.17 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→32.248 Å / FOM work R set: 0.817 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1885 4.98 %
Rwork0.1955 --
obs0.1974 37835 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 303.97 Å2 / Biso mean: 118.62 Å2 / Biso min: 45.75 Å2
Refinement stepCycle: LAST / Resolution: 3.2→32.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8766 1884 0 2 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311102
X-RAY DIFFRACTIONf_angle_d0.87215416
X-RAY DIFFRACTIONf_chiral_restr0.0531618
X-RAY DIFFRACTIONf_plane_restr0.0041716
X-RAY DIFFRACTIONf_dihedral_angle_d20.3254272
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4383X-RAY DIFFRACTIONPOSITIONAL0.005
12F4383X-RAY DIFFRACTIONPOSITIONAL0.005
21D429X-RAY DIFFRACTIONPOSITIONAL0.003
22I429X-RAY DIFFRACTIONPOSITIONAL0.003
31B302X-RAY DIFFRACTIONPOSITIONAL0.001
32G302X-RAY DIFFRACTIONPOSITIONAL0.001
41C211X-RAY DIFFRACTIONPOSITIONAL0.01
42H211X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.28640.37061460.281527392885100
3.2864-3.38310.27421350.243727682903100
3.3831-3.49210.24711580.214627232881100
3.4921-3.61680.2661370.208327572894100
3.6168-3.76140.2341450.204727572902100
3.7614-3.93230.27041410.194727782919100
3.9323-4.13920.22741600.187227412901100
4.1392-4.39790.2161330.183427632896100
4.3979-4.73650.22041490.189227742923100
4.7365-5.21140.2781460.196827892935100
5.2114-5.96140.23021420.212627892931100
5.9614-7.49510.26051510.216927742925100
7.4951-32.24990.18021420.16242798294098
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)
11.77640.4957-0.82561.4949-0.13332.4996-0.0161-0.0140.4143-0.02910.0569-0.0286-0.08380.3114-0.04850.6712-0.104-0.41970.87050.07860.969822.4799-46.8784237.2242
20.9137-1.138-0.48323.0638-0.071-0.00640.04990.2545-0.0279-0.3341-0.19530.49450.007-0.03130.16841.1031-0.1047-0.49060.9730.13650.9077-2.4615-35.7174210.3124
35.0888-5.1289-2.75465.06182.95446.32660.5508-0.72860.32440.6383-0.13930.4955-0.37630.5209-0.571.3647-0.302-0.35931.29950.07421.6023-8.0515-36.7652221.9247
43.08681.8646-4.90055.9517-2.2657.8054-1.08291.24780.1166-0.14460.72240.48950.9466-1.1652-0.02950.9107-0.0879-0.19941.1490.10321.10375.212-59.7796239.1728
59.66964.875-6.41084.3969-6.41599.40750.66131.443-0.85580.9881-0.2061.3172-0.1892-1.4241-0.0691.40070.2353-0.29781.79680.00391.8163-22.5946-29.1026219.8725
62.43771.6533-1.17558.46031.26031.25510.10661.92580.41860.245-0.7387-0.3064-0.72370.330.30571.25190.2135-0.211.70010.50251.223-0.9977-49.0081225.628
73.1511-4.6122-3.28739.45344.67913.5088-1.0118-0.40120.4005-0.32441.35470.25680.8160.061-0.84161.1096-0.1094-0.22651.133-0.08320.96378.9132-60.829241.477
81.61640.40520.72571.4124-0.01472.3903-0.0799-0.0075-0.3869-0.020.07150.07670.0999-0.2597-0.1020.6919-0.0989-0.190.8809-0.08531.009415.9853-13.6153166.1365
90.9058-1.08950.26973.13540.3393-0.05410.00940.21070.0529-0.3895-0.1831-0.51010.0212-0.0058-0.02671.1129-0.1068-0.10140.989-0.11170.970840.9081-24.7806139.209
102.8664-2.84972.17713.3537-0.316.38180.0095-0.61360.20580.73740.0078-0.18120.0251-0.68160.5611.2547-0.3328-0.11561.3020.03691.640446.5187-23.7141150.8071
117.76670.36511.65211.93352.4834.7921-1.07911.1989-0.0861-0.24690.8157-0.4415-1.15081.2868-1.20571.0579-0.1351-0.47221.2108-0.08131.063733.251-0.708168.1038
123.41552.5584.22238.0939-0.92437.85830.77861.21560.86270.2854-0.4033-1.45830.36561.5721-0.6651.35850.1649-0.21681.6491-0.07541.840961.0509-31.3851148.7388
134.3649-5.55060.91237.0368-1.21250.1773-0.08920.7278-0.19470.4271-0.5038-0.18370.4096-0.2156-0.03821.26120.2036-0.28951.5309-0.38631.291439.4645-11.4767154.523
147.46410.44952.17027.5762-3.15728.0974-0.6145-0.3226-0.5021-0.27551.0421-0.3411-1.1980.11540.48931.0218-0.0781-0.40891.10810.02290.875229.57280.3412170.3858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 16 THROUGH 214 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 215 THROUGH 553 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID -2 THROUGH 12 )
4X-RAY DIFFRACTION4CHAIN C AND (RESID 1 THROUGH 10 )
5X-RAY DIFFRACTION5CHAIN D AND (RESID 1 THROUGH 7 )
6X-RAY DIFFRACTION6CHAIN D AND (RESID 8 THROUGH 15 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 16 THROUGH 21 )
8X-RAY DIFFRACTION8CHAIN F AND (RESID 16 THROUGH 214 )
9X-RAY DIFFRACTION9CHAIN F AND (RESID 215 THROUGH 553 )
10X-RAY DIFFRACTION10CHAIN G AND (RESID -2 THROUGH 12 )
11X-RAY DIFFRACTION11CHAIN H AND (RESID 1 THROUGH 10 )
12X-RAY DIFFRACTION12CHAIN I AND (RESID 1 THROUGH 7 )
13X-RAY DIFFRACTION13CHAIN I AND (RESID 8 THROUGH 15 )
14X-RAY DIFFRACTION14CHAIN I AND (RESID 16 THROUGH 21 )

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