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- PDB-3k1l: Crystal Structure of FANCL -

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Basic information

Entry
Database: PDB / ID: 3k1l
TitleCrystal Structure of FANCL
ComponentsFancl
KeywordsLIGASE / UBC / RING / RWD
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / protein monoubiquitination / interstrand cross-link repair / ubiquitin protein ligase activity / DNA repair / metal ion binding / nucleus
Similarity search - Function
Copper Amine Oxidase; Chain A, domain 1 - #30 / Copper Amine Oxidase; Chain A, domain 1 - #40 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 ...Copper Amine Oxidase; Chain A, domain 1 - #30 / Copper Amine Oxidase; Chain A, domain 1 - #40 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / Copper Amine Oxidase; Chain A, domain 1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / : / CITRIC ACID / AT07283p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsCole, A.R. / Walden, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: The structure of the catalytic subunit FANCL of the Fanconi anemia core complex
Authors: Cole, A.R. / Lewis, L.P.C. / Walden, H.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 4, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fancl
A: Fancl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,63424
Polymers87,5512
Non-polymers4,08322
Water23413
1
B: Fancl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,01613
Polymers43,7751
Non-polymers2,24112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fancl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,61811
Polymers43,7751
Non-polymers1,84210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Fancl
A: Fancl
hetero molecules

B: Fancl
A: Fancl
hetero molecules

B: Fancl
A: Fancl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,90272
Polymers262,6526
Non-polymers12,25066
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area29060 Å2
ΔGint-331 kcal/mol
Surface area112130 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-94 kcal/mol
Surface area39210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.680, 188.680, 259.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROchain B and (resseq 107:299 or resseq 310:333 or resseq...BA107 - 299107 - 299
12ARGARGLYSLYSchain B and (resseq 107:299 or resseq 310:333 or resseq...BA310 - 333310 - 333
13CYSCYSMETMETchain B and (resseq 107:299 or resseq 310:333 or resseq...BA338 - 351338 - 351
14PHEPHECYSCYSchain B and (resseq 107:299 or resseq 310:333 or resseq...BA361 - 364361 - 364
15LEULEUASPASPchain B and (resseq 107:299 or resseq 310:333 or resseq...BA371 - 381371 - 381
21ARGARGPROPROchain A and (resseq 107:299 or resseq 310:333 or resseq...AB107 - 299107 - 299
22ARGARGLYSLYSchain A and (resseq 107:299 or resseq 310:333 or resseq...AB310 - 333310 - 333
23CYSCYSMETMETchain A and (resseq 107:299 or resseq 310:333 or resseq...AB338 - 351338 - 351
24PHEPHECYSCYSchain A and (resseq 107:299 or resseq 310:333 or resseq...AB361 - 364361 - 364
25LEULEUASPASPchain A and (resseq 107:299 or resseq 310:333 or resseq...AB371 - 381371 - 381
DetailsThe protein was crystallised from a monomeric state as verified by gel filtration. By analysis of the structure and previous knowledge of the protein author believe the crystal contacts of the protein to be crystallographic artefacts and not indicative of a higher quaternary structure.

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Fancl / / AT07283p / E3 Ligase


Mass: 43775.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SUMO tag inserted into pET vector / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG12812 / Plasmid: modified pET 28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8T913, ubiquitin-protein ligase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 33 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Au
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 5.07399 Å3/Da / Density % sol: 75.7587 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M Ammonium Citrate, 100mM Bis-Tris-Propane, 1mM TCEP, 0.050mM ZNCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0397 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 3.2→77.926 Å / Num. all: 29126 / Num. obs: 25772 / % possible obs: 98.8 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 12.2 % / Biso Wilson estimate: 85.94 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 6.3
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→77.926 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.831 / SU ML: 0.65 / Isotropic thermal model: Isotropic / σ(F): 1.13 / Phase error: 24.08 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2466 2709 5.13 %
Rwork0.2051 --
obs0.2072 25772 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.867 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 98.532 Å2
Baniso -1Baniso -2Baniso -3
1--5.944 Å2-0 Å20 Å2
2---5.944 Å2-0 Å2
3---11.889 Å2
Refinement stepCycle: LAST / Resolution: 3.2→77.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 102 13 6079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086190
X-RAY DIFFRACTIONf_angle_d1.1268391
X-RAY DIFFRACTIONf_dihedral_angle_d18.8652299
X-RAY DIFFRACTIONf_chiral_restr0.073933
X-RAY DIFFRACTIONf_plane_restr0.0041070
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1979X-RAY DIFFRACTIONPOSITIONAL0.04
12A1979X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.2580.3631420.322612275493
3.258-3.3210.3671660.3142634280093
3.321-3.3890.3971430.2882659280293
3.389-3.4620.271320.2712647277993
3.462-3.5430.2581650.2412582274793
3.543-3.6320.2541700.2422622279293
3.632-3.730.2661400.2282643278393
3.73-3.8390.2511570.2252599275693
3.839-3.9630.2631150.2062685280093
3.963-4.1050.2161240.1892646277093
4.105-4.2690.2031290.182625275493
4.269-4.4640.1871710.1562621279293
4.464-4.6990.1761360.1592634277093
4.699-4.9930.1871530.1472655280893
4.993-5.3790.1851270.1532656278393
5.379-5.920.2221170.1772667278493
5.92-6.7760.2241380.1922650278894
6.776-8.5350.231650.1912607277292
8.535-77.9490.2771190.2012643276292
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)
12.12863.03720.43646.2294-1.27512.7027-0.19020.3565-0.1956-0.03520.1375-0.1483-0.43670.7052-0.13671.1118-0.14920.18391.38540.02041.352516.839141.084255.9016
22.8604-2.8027-0.61774.65270.36371.2223-0.31950.5125-0.8340.36040.30011.76670.0715-0.22690.19420.56120.1106-0.01280.9725-0.04760.926110.908924.563962.468
32.9158-1.8476-0.71340.53710.38210.68330.0583-0.3323-0.258-0.11280.0950.1665-0.0225-0.2478-0.11460.7049-0.0845-0.05570.87-0.04780.674822.938119.851756.7765
40.8127-1.21780.77870.2756-1.09581.842-0.18610.0654-0.3353-0.23060.15990.34320.43290.2491-0.05540.7338-0.10290.03450.8308-0.03880.794136.2235-3.529745.9817
51.89621.8142-3.6970.7824-3.3390.9383-0.4849-0.57940.3491-0.2933-0.4517-0.66440.2954-0.14340.10421.3178-0.3164-0.13991.24610.03261.164739.5066-23.525164.5997
61.26850.38150.15490.3627-0.45761.18390.29070.3848-0.1279-0.1711-0.1036-0.04180.14160.3397-0.24160.61680.1196-0.05940.9662-0.03260.620152.6775-6.499758.8498
72.3754-1.2877-3.24694.5607-0.54071.8903-0.57330.8789-0.2319-0.0142-1.0112-0.0551-0.85930.45971.20391.1278-0.1105-0.28871.0918-0.02380.561346.84112.979356.1677
82.0262-2.62960.65063.9892-2.70644.5776-0.21160.23790.7282-0.1185-0.07260.5543-0.2723-1.35580.0850.96190.2207-0.26130.96150.11240.803363.0349-7.618171.5664
92.1019-1.6257-0.1231.0711-0.23230.9151-0.3056-0.66820.50230.32030.1571-0.2044-0.12070.00370.11410.8250.0547-0.08161.06050.13960.853667.3372-15.848378.213
102.0573-1.59830.11742.3806-3.19039.5447-0.4420.55920.1401-0.0056-0.5618-0.13350.46221.20380.53050.95-0.0323-0.21581.2274-0.04840.900165.8455-21.01769.6903
110.69551.65020.4172.69910.95151.0695-0.097-0.14120.17590.03680.16990.37550.0176-0.0746-0.06710.6675-0.0245-0.06270.88010.1030.645827.8358-10.146776.2604
12-0.37530.21930.7272.16120.05572.68750.0273-0.46930.06780.43480.1660.2337-0.1769-0.1201-0.13470.783-0.0303-0.04881.0179-0.11880.774731.2219.897587.8331
136.47363.7586-0.88424.32981.08257.2682-1.05020.41540.4843-1.56590.33180.4576-0.6753-0.22711.12561.5116-0.2728-0.27031.4758-0.16751.460525.287637.867969.5
142.47971.373-0.10150.651.54741.86290.0256-0.3930.460.03030.08070.0969-0.02370.3424-0.19780.7923-0.1727-0.05070.8548-0.13110.757844.223928.97374.6897
151.51860.71.4390.9037-1.77041.9630.54630.33410.27230.2674-0.37930.60670.81350.25190.22330.9402-0.21660.18811.0559-0.4690.738964.123529.200469.944
161.50690.3662-1.85051.48-0.42880.4242-0.0484-0.2763-0.2889-0.02320.36160.15010.06260.315-0.15030.7529-0.0936-0.04060.9005-0.06260.650457.695524.288660.4908
17-0.96093.99143.87085.83850.23833.5094-0.91440.67510.78530.22551.12421.0021-0.2814-0.7212-0.16540.7356-0.09590.05471.10120.05911.062745.430524.203954.1173
183.9035-0.35830.31851.68630.00311.07960.4040.88-0.6003-0.4084-0.08350.102-0.38450.6752-0.23470.6142-0.1476-0.04470.8253-0.03050.678559.94633.114953.8263
19-0.6174-2.06240.17554.5713.21881.1590.53740.10090.83590.71640.4456-0.73870.6741-0.5579-0.57951.2579-0.30280.26870.84350.03141.216433.770135.801255.1619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 104:108)A104 - 108
2X-RAY DIFFRACTION2(chain A and resid 109:129)A109 - 129
3X-RAY DIFFRACTION3(chain A and resid 130:199)A130 - 199
4X-RAY DIFFRACTION4(chain A and resid 200:299)A200 - 299
5X-RAY DIFFRACTION5(chain A and resid 300:308)A300 - 308
6X-RAY DIFFRACTION6(chain A and resid 309:375)A309 - 375
7X-RAY DIFFRACTION7(chain A and resid 376:381)A376 - 381
8X-RAY DIFFRACTION8(chain B and resid 6:41)B6 - 41
9X-RAY DIFFRACTION9(chain B and resid 42:86)B42 - 86
10X-RAY DIFFRACTION10(chain B and resid 87:94)B87 - 94
11X-RAY DIFFRACTION11(chain B and resid 107:198)B107 - 198
12X-RAY DIFFRACTION12(chain B and resid 199:299)B199 - 299
13X-RAY DIFFRACTION13(chain B and resid 300:308)B300 - 308
14X-RAY DIFFRACTION14(chain B and resid 309:381)B309 - 381
15X-RAY DIFFRACTION15(chain A and resid 5:16)A5 - 16
16X-RAY DIFFRACTION16(chain A and resid 17:61)A17 - 61
17X-RAY DIFFRACTION17(chain A and resid 62:68)A62 - 68
18X-RAY DIFFRACTION18(chain A and resid 69:96)A69 - 96
19X-RAY DIFFRACTION19(chain A and resid 97:102)A97 - 102

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