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- PDB-4rid: Human FAN1 nuclease -

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Basic information

Entry
Database: PDB / ID: 4rid
TitleHuman FAN1 nuclease
ComponentsFanconi-associated nuclease 1
KeywordsHYDROLASE / nuclease
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / 5'-3' exonuclease activity / phosphodiesterase I activity / interstrand cross-link repair / intercellular bridge / nucleotide-excision repair ...flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / 5'-3' exonuclease activity / phosphodiesterase I activity / interstrand cross-link repair / intercellular bridge / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / cilium / DNA repair / magnesium ion binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain ...: / : / : / Fanconi-associated nuclease 1, SAP subdomain / Fanconi-associated nuclease 1, TPR domain / Fanconi-associated nuclease 1-like / : / FAN1, HTH domain / VRR-NUC domain / VRR-NUC domain / VRR_NUC / Rad18-like CCHC zinc finger / tRNA endonuclease-like domain superfamily / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile.
Similarity search - Domain/homology
Fanconi-associated nuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsPavletich, N.P. / Wang, R.
CitationJournal: Science / Year: 2014
Title: DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1.
Authors: Wang, R. / Persky, N.S. / Yoo, B. / Ouerfelli, O. / Smogorzewska, A. / Elledge, S.J. / Pavletich, N.P.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: Fanconi-associated nuclease 1
B: Fanconi-associated nuclease 1


Theoretical massNumber of molelcules
Total (without water)145,9162
Polymers145,9162
Non-polymers00
Water00
1
A: Fanconi-associated nuclease 1


Theoretical massNumber of molelcules
Total (without water)72,9581
Polymers72,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fanconi-associated nuclease 1


Theoretical massNumber of molelcules
Total (without water)72,9581
Polymers72,9581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Fanconi-associated nuclease 1
B: Fanconi-associated nuclease 1

A: Fanconi-associated nuclease 1
B: Fanconi-associated nuclease 1


Theoretical massNumber of molelcules
Total (without water)291,8324
Polymers291,8324
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9710 Å2
ΔGint-4 kcal/mol
Surface area107100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.882, 156.885, 205.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A371 - 426
2112B371 - 426
1122A538 - 552
2122B538 - 552
1132A427 - 459
2132B427 - 459
1142A533 - 537
2142B533 - 537
1152A460 - 532
2152B460 - 532
1162A593 - 773
2162B593 - 773
1172A774 - 834
2172B774 - 834
1182A956 - 1017
2182B956 - 1017
1192A572 - 592
2192B572 - 592
11102A835 - 955
21102B835 - 955

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein Fanconi-associated nuclease 1 / FANCD2/FANCI-associated nuclease 1 / Myotubularin-related protein 15


Mass: 72958.062 Da / Num. of mol.: 2 / Fragment: unp residues 370-1009
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, KIAA1018, MTMR15 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y2M0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, phosphodiesterase I

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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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2013
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.3→70 Å / Num. all: 68933 / Num. obs: 68520 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Χ2: 0.434 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.426.70.71469040.415199.7
3.42-3.557.20.48268620.4321100
3.55-3.727.10.35169260.4361100
3.72-3.916.90.22868610.451199.9
3.91-4.166.50.16968670.452199.5
4.16-4.487.20.11868790.465199.9
4.48-4.937.10.09268950.46199.9
4.93-5.646.60.08168720.447199.6
5.64-7.117.10.06868330.419199.6
7.11-706.70.03166210.356195.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.266 / SU ML: 0.407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1076 3.1 %RANDOM
Rwork0.2457 ---
obs0.2471 33593 96.05 %-
all-34975 --
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 266.94 Å2 / Biso mean: 115.65 Å2 / Biso min: 63.03 Å2
Baniso -1Baniso -2Baniso -3
1--5.7 Å2-0 Å20 Å2
2--2.92 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 0 0 9981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910186
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.95913770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94423.181481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.704151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8781591
X-RAY DIFFRACTIONr_chiral_restr0.0930.21546
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217621
X-RAY DIFFRACTIONr_mcbond_it2.5275.7634965
X-RAY DIFFRACTIONr_mcangle_it4.53712.9596194
X-RAY DIFFRACTIONr_scbond_it2.3525.7715220
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1484TIGHT POSITIONAL0.030.05
1248MEDIUM POSITIONAL0.030.5
1224TIGHT THERMAL11.999
1248MEDIUM THERMAL12.9199
260MEDIUM POSITIONAL0.040.5
260TIGHT THERMAL11.5599
260MEDIUM THERMAL10.4199
3136MEDIUM POSITIONAL0.030.5
3132TIGHT THERMAL20.7899
3136MEDIUM THERMAL20.6299
421MEDIUM POSITIONAL0.030.5
420TIGHT THERMAL28.0299
421MEDIUM THERMAL23.7999
5233MEDIUM POSITIONAL0.020.5
5256TIGHT THERMAL54.9599
5233MEDIUM THERMAL51.0599
6788MEDIUM POSITIONAL0.040.5
6724TIGHT THERMAL16.2299
6788MEDIUM THERMAL16.2699
7171MEDIUM POSITIONAL0.030.5
7180TIGHT THERMAL4.1499
7171MEDIUM THERMAL5.2699
8210MEDIUM POSITIONAL0.040.5
8216TIGHT THERMAL3.999
8210MEDIUM THERMAL4.4499
986MEDIUM POSITIONAL0.040.5
984TIGHT THERMAL4.5399
986MEDIUM THERMAL5.0899
10473MEDIUM POSITIONAL0.040.5
10484TIGHT THERMAL3.7199
10473MEDIUM THERMAL4.4299
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 64 -
Rwork0.329 2216 -
all-2280 -
obs--86.96 %

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