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- PDB-4ry3: Crystal structure of human Fanconi-associated nuclease 1 -

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Basic information

Entry
Database: PDB / ID: 4ry3
TitleCrystal structure of human Fanconi-associated nuclease 1
ComponentsFanconi-associated nuclease 1
KeywordsHYDROLASE / Endonuclease 5'-3'exonulease / FANCD2 / FAN1
Function / homology
Function and homology information


flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair ...flap-structured DNA binding / phosphodiesterase I / 5'-flap endonuclease activity / phosphodiesterase I activity / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / ubiquitin-modified protein reader activity / intercellular bridge / interstrand cross-link repair / nucleotide-excision repair / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / DNA repair / magnesium 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: 2.802 Å
AuthorsYan, P.X. / Huo, Y.G. / Jiang, T.
CitationJournal: Protein Cell / Year: 2015
Title: Crystal structure of human Fanconi-associated nuclease 1.
Authors: Yan, P.X. / Huo, Y.G. / Jiang, T.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fanconi-associated nuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0482
Polymers73,8531
Non-polymers1951
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fanconi-associated nuclease 1
hetero molecules

A: Fanconi-associated nuclease 1
hetero molecules

A: Fanconi-associated nuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,1446
Polymers221,5593
Non-polymers5853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area10530 Å2
ΔGint-100 kcal/mol
Surface area82170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.082, 161.082, 161.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 73852.992 Da / Num. of mol.: 1 / Fragment: UNP residues 371-1010
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, KIAA1018, MTMR15 / Plasmid: pPICZB / Production host: Pichia pastoris (fungus) / Strain (production host): X33
References: UniProt: Q9Y2M0, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, phosphodiesterase I
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt

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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: 4.72 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 2.5M sodium acetate, 0.1M Bis-Tris propane, 10% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.068 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 34542 / Num. obs: 34401 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 34.15 Å2
Reflection shellResolution: 2.8→2.85 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.802→19.98 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1727 5.04 %
Rwork0.2078 --
obs0.2097 34261 99.6 %
all-34399 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.9467 Å2
Refinement stepCycle: LAST / Resolution: 2.802→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 1 0 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094865
X-RAY DIFFRACTIONf_angle_d1.2526580
X-RAY DIFFRACTIONf_dihedral_angle_d17.3431804
X-RAY DIFFRACTIONf_chiral_restr0.083739
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8015-2.88370.32691240.27632665278997
2.8837-2.97650.32651220.253526822804100
2.9765-3.08250.33651230.24426852808100
3.0825-3.20550.32551390.262527142853100
3.2055-3.35070.30621480.23826982846100
3.3507-3.52650.27721440.213726912835100
3.5265-3.74610.26971540.201527172871100
3.7461-4.03310.21861500.184726812831100
4.0331-4.4350.20041620.175727202882100
4.435-5.06750.1771510.167527272878100
5.0675-6.35040.22511630.211527342897100
6.3504-19.98030.20111470.18962820296799
Refinement TLS params.Method: refined / Origin x: 24.3429 Å / Origin y: -13.0969 Å / Origin z: 97.0571 Å
111213212223313233
T0.1169 Å20.0802 Å2-0.0778 Å2-0.2214 Å2-0.0346 Å2---0.0341 Å2
L0.0585 °20.0572 °20.1208 °2-0.0201 °2-0.0192 °2--0.2176 °2
S0.0009 Å °-0.1092 Å °-0.0387 Å °-0.0208 Å °-0.0033 Å °0.0478 Å °-0.1036 Å °-0.1748 Å °0.1787 Å °
Refinement TLS groupSelection details: all

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