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- PDB-5lcl: STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH C8-amin... -

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Basic information

Entry
Database: PDB / ID: 5lcl
TitleSTRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH C8-aminofluorene- GUANINE CONTAINING DNA
Components
  • (DNA repair protein ...) x 2
  • DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-3')
  • GCTCTAC(8AF)TCATCA
KeywordsDNA BINDING PROTEIN / Nucleotide excision repair DNA damage recognition
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / base-excision repair / damaged DNA binding / DNA damage response / zinc ion binding / nucleus
Similarity search - Function
XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein RAD14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchneider, S. / Carell, T. / Ebert, C. / Simon, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Chembiochem / Year: 2017
Title: Structural Insights into the Recognition of N(2) -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14.
Authors: Ebert, C. / Simon, N. / Schneider, S. / Carell, T.
History
DepositionJun 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _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
A: DNA repair protein RAD14
B: DNA repair protein RAD14
C: GCTCTAC(8AF)TCATCA
D: DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8146
Polymers66,6834
Non-polymers1312
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.205, 53.205, 130.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 188 - 299

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA1 - 112
2BB188 - 299

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-7.0E-6, -0.999991, 0.00417), (-1, 9.0E-6, 0.000486), (-0.000486, -0.00417, -0.999991)79.83881, 79.81107, -66.62171

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Components

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DNA repair protein ... , 2 types, 2 molecules AB

#1: Protein DNA repair protein RAD14


Mass: 14224.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RAD14, YMR201C, YM8325.02C / Plasmid: pIBA35 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P28519
#2: Protein DNA repair protein RAD14


Mass: 43116.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RAD14, YMR201C, YM8325.02C / Plasmid: pIBA35 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P28519

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain GCTCTAC(8AF)TCATCA


Mass: 4668.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus)
#4: DNA chain DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-3')


Mass: 4674.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus)

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Non-polymers , 2 types, 51 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.22M ammonium nitrate 38% 2-methyl-1,3,-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→49.3 Å / Num. obs: 18314 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.6 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSVERSION Oct 15, 2015data reduction
XDSVERSION Oct 15, 2015data scaling
REFMAC5.8.0151phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G32

5g32


Resolution: 2.2→49.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.418 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25555 895 4.9 %RANDOM
Rwork0.21651 ---
obs0.2184 17418 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 579 2 49 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0163226
X-RAY DIFFRACTIONr_bond_other_d0.0040.022412
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.6624597
X-RAY DIFFRACTIONr_angle_other_deg1.61535627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95124.393107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3291513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212861
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02732
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1052.296910
X-RAY DIFFRACTIONr_mcbond_other1.0862.293909
X-RAY DIFFRACTIONr_mcangle_it1.8123.4281135
X-RAY DIFFRACTIONr_mcangle_other1.8153.4331136
X-RAY DIFFRACTIONr_scbond_it0.8382.0962316
X-RAY DIFFRACTIONr_scbond_other0.8382.0962315
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3683.1123461
X-RAY DIFFRACTIONr_long_range_B_refined3.47421.5533860
X-RAY DIFFRACTIONr_long_range_B_other3.46121.4923852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1779 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.350.5
medium thermal1.292
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 62 -
Rwork0.301 1168 -
obs--92.07 %
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)
12.09371.7752-3.26353.5846-4.363411.2403-0.04540.215-0.1926-0.21840.1741-0.05740.34070.117-0.12870.07280.02650.00750.0805-0.02530.086849.831650.9892-66.1831
25.90921.939-0.28428.3541-6.09064.81890.2044-0.0117-0.00490.2949-0.11120.0767-0.10480.1052-0.09320.10270.01140.0180.0469-0.00450.034847.732654.7232-63.4515
34.74740.3417-2.62182.24910.33423.58390.13250.15180.08530.0239-0.14240.0996-0.0513-0.42660.00990.04880.0059-0.01090.067800.033935.58956.6331-51.8493
43.8040.7463.1782.96871.54716.37560.02230.05490.16530.0494-0.05770.02080.1295-0.07360.03530.02120.01040.01850.01610.02160.033840.818554.8795-48.2784
53.4461-1.37531.655610.7765.56188.7599-0.10850.28110.43170.0494-0.13840.8055-0.8026-0.56570.24680.19430.03450.03250.36520.11550.344521.667161.2618-53.8942
613.1142.7043-0.62760.5778-0.1170.03780.0797-0.40840.0768-0.0529-0.0569-0.0195-0.05070.0326-0.02280.39920.0039-0.00460.2535-0.02210.242716.255571.0174-44.7049
75.27771.4332-3.24312.9987-3.1629.65170.2089-0.2204-0.20570.26790.0015-0.10310.06050.3054-0.21040.05640.015-0.020.02980.00280.078428.812430.0156-0.6139
89.59823.0872-5.20785.0602-1.32896.3314-0.00970.262-0.0848-0.16290.20360.03370.218-0.0159-0.19380.07740.0230.01650.04390.01550.046625.044231.995-3.1998
92.122-0.1931-0.2184.3353-2.19352.6302-0.0882-0.03520.10340.14540.09920.1715-0.4076-0.0908-0.0110.10260.0181-0.00080.02730.00210.047422.315144.3142-14.6622
102.98561.46011.95554.21143.7725.9886-0.1119-0.0105-0.00510.01140.07340.2007-0.25860.02960.03860.0390.01010.02160.01770.01930.029424.923738.9688-18.521
1111.9712-3.51252.70797.5024-0.37197.33710.15240.43190.38520.3751-0.14980.432-0.2959-0.4648-0.00260.36650.01980.07890.1845-0.01070.315719.550257.7576-12.6492
123.7403-4.4347-6.24125.44917.331410.44540.127-0.1502-0.0102-0.1815-0.06690.179-0.24140.3325-0.060.3083-0.0228-0.04520.4469-0.03690.39689.129762.6987-24.0687
134.0506-3.51460.57374.44810.78621.2669-0.4632-0.3595-0.50520.37580.0541.04390.0134-0.20510.40920.19930.07060.07640.1198-0.05110.333330.847359.0737-34.2233
1410.4244-2.14885.96121.1299-2.48235.75310.33890.52930.1817-0.22270.06990.30240.4655-0.1219-0.40880.20940.0025-0.04770.2403-0.08320.383515.588544.9629-34.8881
152.3237-4.27251.04539.1458-0.78911.48480.37690.21880.3022-0.8964-0.3992-0.57390.11910.17680.02230.20350.0121-0.11120.20840.05150.28420.750749.0431-32.5298
162.34880.2711-3.2928.50710.14394.65870.0808-0.40760.33920.48510.3604-0.0442-0.12930.5881-0.44120.26990.0522-0.0550.178-0.06850.26834.861464.217-31.9333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 208
2X-RAY DIFFRACTION2A209 - 218
3X-RAY DIFFRACTION3A219 - 247
4X-RAY DIFFRACTION4A248 - 278
5X-RAY DIFFRACTION5A279 - 295
6X-RAY DIFFRACTION6A296 - 300
7X-RAY DIFFRACTION7B188 - 208
8X-RAY DIFFRACTION8B209 - 218
9X-RAY DIFFRACTION9B219 - 245
10X-RAY DIFFRACTION10B248 - 278
11X-RAY DIFFRACTION11B279 - 295
12X-RAY DIFFRACTION12B296 - 301
13X-RAY DIFFRACTION13C1 - 9
14X-RAY DIFFRACTION14C10 - 14
15X-RAY DIFFRACTION15D1 - 9
16X-RAY DIFFRACTION16D10 - 14

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