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- PDB-4r89: Crystal structure of paFAN1 - 5' flap DNA complex with Manganase -

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Basic information

Entry
Database: PDB / ID: 4r89
TitleCrystal structure of paFAN1 - 5' flap DNA complex with Manganase
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*AP*C)-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 / MOLECULAR REPLACEMENT / Resolution: 4.002 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 / _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: 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*AP*C)-3')
E: Uncharacterized protein
F: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')
G: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
H: 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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,14012
Polymers157,9208
Non-polymers2204
Water00
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*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0706
Polymers78,9604
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-56 kcal/mol
Surface area34100 Å2
MethodPISA
2
E: Uncharacterized protein
F: DNA (5'-D(P*AP*CP*CP*AP*GP*AP*CP*AP*CP*AP*CP*AP*TP*TP*C)-3')
G: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*AP*TP*TP*G)-3')
H: 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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0706
Polymers78,9604
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-56 kcal/mol
Surface area34120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.115, 106.944, 107.541
Angle α, β, γ (deg.)90.00, 89.84, 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 17:553 ) AND (NOT ELEMENT H)
211CHAIN E AND (RESSEQ 17:553 ) AND (NOT ELEMENT H)
112CHAIN D AND (RESSEQ 1:22 ) AND (NOT ELEMENT H)
212CHAIN H AND (RESSEQ 1:22 ) AND (NOT ELEMENT H)
113CHAIN B AND (RESSEQ -2:12 ) AND (NOT ELEMENT H)
213CHAIN F AND (RESSEQ -2:12 ) AND (NOT ELEMENT H)
114CHAIN C AND (RESSEQ 1:10 ) AND (NOT ELEMENT H)
214CHAIN G AND (RESSEQ 1:10 ) AND (NOT ELEMENT H)

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 / 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*AP*C)-3')


Mass: 6711.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 2.95 Å3/Da / Density % sol: 58.36 %
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: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2014
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 15502 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 157.59 Å2
Reflection shellHighest resolution: 4 Å / % possible all: 99.7

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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: MOLECULAR REPLACEMENT / Resolution: 4.002→44.644 Å / SU ML: 0.57 / σ(F): 1.36 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 771 4.99 %
Rwork0.2238 --
obs0.2265 15461 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 353.75 Å2 / Biso mean: 150.4014 Å2 / Biso min: 14.81 Å2
Refinement stepCycle: LAST / Resolution: 4.002→44.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8750 1922 4 0 10676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411138
X-RAY DIFFRACTIONf_angle_d0.9115464
X-RAY DIFFRACTIONf_chiral_restr0.0461622
X-RAY DIFFRACTIONf_plane_restr0.0031714
X-RAY DIFFRACTIONf_dihedral_angle_d19.7244286
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4375X-RAY DIFFRACTIONPOSITIONAL0.005
12E4375X-RAY DIFFRACTIONPOSITIONAL0.005
21D448X-RAY DIFFRACTIONPOSITIONAL0.003
22H448X-RAY DIFFRACTIONPOSITIONAL0.003
31B302X-RAY DIFFRACTIONPOSITIONAL0.003
32F302X-RAY DIFFRACTIONPOSITIONAL0.003
41C211X-RAY DIFFRACTIONPOSITIONAL0.003
42G211X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0015-4.25210.32441370.3062301243894
4.2521-4.58010.36231380.270624392577100
4.5801-5.04040.30971300.264824792609100
5.0404-5.76840.30891150.267324772592100
5.7684-7.26260.36071180.262324952613100
7.2626-44.64710.20731330.16212499263299
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)
12.098-0.9235-0.19693.5461.4032.00870.29620.25380.21610.3450.0995-1.008-0.70330.6897-0.18691.4681-0.319-0.10161.3059-0.19351.5538213.8758-76.6986129.5889
2-0.90131.1486-0.61022.78730.18085.18490.1675-0.24060.3194-0.00380.073-0.07660.02720.574-0.00431.328-0.00150.14550.9812-0.07981.0311189.5432-91.4287152.4955
31.76451.0432-0.15755.4836-2.24743.9230.3169-0.2395-0.0273-0.74920.1320.3281-0.0088-0.7076-0.21830.74490.2317-0.06061.1311-0.11950.8761172.9794-86.6985128.7026
44.3044-2.63840.27169.1703-7.15146.03311.09510.21470.8031-0.0549-1.8593-2.61060.35941.80391.45621.96470.02460.10371.4831-0.0411.858188.8773-99.764138.4226
51.5783-3.6807-2.6598.12655.76663.941-2.07180.4112-1.1570.28881.14091.13591.24530.05560.96882.2905-0.2130.73731.0846-0.14292.4391209.9875-95.55119.165
63.33412.47082.15483.2454-1.86369.59850.63352.2083-1.2715-0.00041.0148-0.22182.005-0.1189-0.26961.1893-0.0677-0.07261.1797-0.30951.6641177.0726-112.5687144.1288
72.55033.7111-0.90777.6816-4.1373.9152-0.8711.16912.4035-2.62410.4542-1.96821.99490.4486-0.49541.66870.17560.61851.78870.47012.0439192.8303-103.134139.3054
81.93980.21413.80251.08241.82498.72461.04341.25710.0108-1.0521-0.64544.3063-2.20680.7662-1.28111.6258-0.17430.34841.09050.03742.8527205.6274-92.1696119.5199
91.4112-0.8805-0.18812.8341-1.62313.21740.47470.2787-0.2470.38550.09181.01360.5182-0.83880.17861.501-0.27650.00081.21990.17771.6448151.7205-96.766975.846
10-0.47130.5630.85551.94290.05545.9618-0.0199-0.2045-0.0713-0.24940.22540.61550.1493-0.43590.13591.18790.0059-0.09191.03270.05931.0499176.1037-82.046298.7054
111.49570.11650.41265.32032.91573.94990.1609-0.2318-0.1344-0.4360.197-0.29670.0560.6730.21550.73550.26410.04970.980.13870.789192.6241-86.80374.8877
123.2225-3.3982-0.18068.18515.69155.60850.6691-0.0211-0.406-1.1993-2.04683.4771-0.1204-1.4983-0.49791.8435-0.0728-0.1561.55950.08831.8033176.7549-73.695384.6133
132.1148-3.96092.37627.0762-4.16062.361-1.22410.35981.07721.1670.65750.0385-0.74550.3536-0.51231.9606-0.2333-0.64541.13570.10592.5579155.7342-77.90265.2989
143.70544.0877-1.6868.12430.582.38341.16631.57212.18950.39790.29010.8228-1.59460.70160.68160.9522-0.02130.09871.36010.36091.5664188.5163-60.912390.3769
157.01146.01125.46325.12574.61314.157-0.96230.8441-1.2152-2.68220.45122.7823-0.4853-0.0467-2.41531.76340.3526-0.80861.9365-0.34781.8332172.768-70.350585.5323
163.71421.7314-2.48891.0229-0.50829.05770.43560.06180.3168-0.29130.0314-4.08031.803-0.78130.16221.5178-0.1074-0.43840.94120.07332.377159.9923-81.302865.7259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 17 THROUGH 214 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 215 THROUGH 357 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 358 THROUGH 553 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID -2 THROUGH 12 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 1 THROUGH 10 )
6X-RAY DIFFRACTION6CHAIN D AND (RESID 1 THROUGH 5 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 6 THROUGH 10 )
8X-RAY DIFFRACTION8CHAIN D AND (RESID 11 THROUGH 22 )
9X-RAY DIFFRACTION9CHAIN E AND (RESID 17 THROUGH 214 )
10X-RAY DIFFRACTION10CHAIN E AND (RESID 215 THROUGH 357 )
11X-RAY DIFFRACTION11CHAIN E AND (RESID 358 THROUGH 553 )
12X-RAY DIFFRACTION12CHAIN F AND (RESID -2 THROUGH 12 )
13X-RAY DIFFRACTION13CHAIN G AND (RESID 1 THROUGH 10 )
14X-RAY DIFFRACTION14CHAIN H AND (RESID 1 THROUGH 5 )
15X-RAY DIFFRACTION15CHAIN H AND (RESID 6 THROUGH 10 )
16X-RAY DIFFRACTION16CHAIN H AND (RESID 11 THROUGH 22 )

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