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- PDB-5g32: Structure of Rad14 in complex with acetylaminophenyl-guanine cont... -

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Basic information

Entry
Database: PDB / ID: 5g32
TitleStructure of Rad14 in complex with acetylaminophenyl-guanine containing DNA
Components
  • 5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'
  • 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
  • RAD14
KeywordsCELL CYCLE / DNA REPAIR / NUCLEOTIDE EXCISION REPAIR
Function / homology
Function and homology information


nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Dual incision in TC-NER / base-excision repair / damaged DNA binding / 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 (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSimon, N. / Ebert, C. / Schneider, S.
CitationJournal: Chemistry / Year: 2016
Title: Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14.
Authors: Schneider, S. / Simon, N. / Ebert, C.
History
DepositionApr 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source
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_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 3.0May 15, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_radiation_wavelength / entity_poly / pdbx_seq_map_depositor_info / struct_conn
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_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_atom_name / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_PDB_atom_name / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _diffrn_radiation_wavelength.wavelength / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAD14
B: RAD14
C: 5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'
D: 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
E: 5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'
F: 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4028
Polymers49,2716
Non-polymers1312
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.964, 52.964, 130.945
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A188 - 302
2114B188 - 302

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.001428, -0.999998, -0.001244), (-0.999999, -0.001427, -0.000374), (0.000372, 0.001244, -0.999999)79.44295, 79.50313, -66.76388

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Components

#1: Protein RAD14


Mass: 15612.728 Da / Num. of mol.: 2 / Fragment: RESIDUES 188-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: RAD14, YMR201C, YM8325.02C / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P28519
#2: DNA chain 5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'


Mass: 4638.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'


Mass: 4384.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGUANOSINE AT POS.8 IS MODIFIED AT C8 BY ACETYLAMINOPHENYL

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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: 1.86 Å3/Da / Density % sol: 43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 18268 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.62
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.11 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 20.172 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26552 894 4.9 %RANDOM
Rwork0.21753 ---
obs0.21981 17370 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 1148 2 36 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0163219
X-RAY DIFFRACTIONr_bond_other_d0.0020.022412
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.6564580
X-RAY DIFFRACTIONr_angle_other_deg1.40135631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2325227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54124.579107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94415350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3881512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
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_it1.3772.637914
X-RAY DIFFRACTIONr_mcbond_other1.3682.635913
X-RAY DIFFRACTIONr_mcangle_it2.3023.9461139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1342.5032305
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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: 1824 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.420.5
medium thermal3.752
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 70 -
Rwork0.343 1258 -
obs--99.7 %
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)
11.08441.7863-3.06333.7114-4.316710.6222-0.1090.0552-0.0622-0.28180.11230.06610.31140.296-0.00330.24430.0364-0.0140.2349-0.07080.151749.093750.4054-66.4119
25.77873.9653-2.560112.0937-5.78987.21590.0933-0.2226-0.21360.29660.0602-0.34670.03950.0592-0.15360.1402-0.00120.02930.18730.04970.082847.31854.0529-63.5453
34.96740.2952-3.06132.36870.2615.26520.03990.1810.12340.08430.01370.29530.0398-0.6056-0.05360.175-0.00580.02480.16760.03110.045135.497156.0854-51.5521
45.03870.93194.32062.90570.85696.76810.06640.04620.1063-0.0203-0.088-0.01760.0995-0.0470.02170.12630.01370.03440.15640.02960.016540.831954.3331-48.2014
51.94310.14521.70137.3280.09242.75420.03250.06340.2613-0.2209-0.12920.1007-0.3472-0.28170.09670.22430.0205-0.01190.33680.02160.328721.839560.284-53.3497
64.4744-4.15183.02027.2199-8.812613.6043-0.1386-0.55480.29470.01870.1256-0.05310.2697-0.33980.0130.5142-0.02110.0120.6743-0.080.501317.448169.2979-41.5691
74.38131.7166-4.82751.4038-3.908611.1488-0.0271-0.38170.07880.0282-0.1114-0.11320.09780.31720.13850.21860.0291-0.0740.24290.01390.160529.065230.4105-0.3123
811.46072.6526-7.23464.4286-2.33327.81690.07810.1945-0.19680.14420.0403-0.15040.10170.0816-0.11850.1601-0.00410.02430.16970.03810.094925.387732.1843-3.104
92.84970.14630.16945.5583-2.30523.2825-0.03390.04690.29620.03780.24190.3045-0.4237-0.0874-0.20790.16150.00260.02410.15160.01750.051222.488144.067-14.9543
103.24780.64920.98534.39714.16896.3037-0.10030.04420.0376-0.02930.07550.015-0.13010.08540.02480.16730.00070.02690.14150.04550.019525.125338.6702-18.501
1112.01112.36630.53965.16831.9756.7729-0.302-0.17710.52410.42650.04621.0433-0.6422-0.93550.25590.56140.03090.06970.2626-0.04180.600519.204857.6775-13.4989
129.3146-3.0951-1.58411.3569-0.90376.55170.34520.1789-0.3217-0.0321-0.01810.1715-0.5122-0.2784-0.32710.45480.00360.0280.32960.00640.4669.731562.1173-25.7466
138.7946-4.2713-0.1232.97871.79583.3679-0.505-0.9957-0.86030.35290.14580.61630.2847-0.57260.35920.4724-0.02440.16190.4422-0.07470.320231.734958.1606-34.0932
149.0076-2.39483.01495.1324-3.3792.51530.10180.2139-0.1399-0.07090.24080.72370.0591-0.102-0.34260.3022-0.00420.00940.33660.04890.44315.958743.8944-35.138
153.4606-2.77562.40174.1950.25524.1046-0.04960.30980.4147-0.3112-0.1395-0.3802-0.40110.38830.1890.233-0.02250.01520.2428-0.02690.235920.241742.2233-29.6275
167.0279-5.8239-1.698410.4793-0.90821.4338-0.2158-0.0751.0692-0.18120.60880.05190.1625-0.1262-0.39290.5738-0.0948-0.0660.65890.11340.948731.17761.28-34.0841
171.9166-3.60172.19658.4724-1.86845.65110.07810.1410.3483-0.9269-0.3611-0.6078-0.70480.23990.2830.3790.0314-0.09370.39730.11790.409621.229747.8508-32.6242
185.4721-2.9952-2.94256.45662.4521.77480.2773-0.15760.88780.01390.0201-0.0966-0.16010.0848-0.29740.3788-0.005-0.00260.31390.02870.456835.593363.4966-31.6117
192.2632-1.3201-0.07241.7792.4075.5608-0.0862-0.2513-0.16630.16260.05930.12770.2834-0.17580.02690.1767-0.02050.03380.22090.03010.263837.200859.2409-37.142
208.6884-2.98813.01887.5861-0.23161.1617-0.2498-0.12560.8576-0.8379-0.29691.3446-0.2442-0.05790.54670.7365-0.007-0.06210.53860.07530.653418.085848.2927-32.6674
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 - 302
7X-RAY DIFFRACTION7B188 - 208
8X-RAY DIFFRACTION8B209 - 218
9X-RAY DIFFRACTION9B219 - 245
10X-RAY DIFFRACTION10B248 - 278
11X-RAY DIFFRACTION11B279 - 295
12X-RAY DIFFRACTION12B296 - 302
13X-RAY DIFFRACTION13C1 - 9
14X-RAY DIFFRACTION14C10 - 14
15X-RAY DIFFRACTION15D1 - 6
16X-RAY DIFFRACTION16D7 - 14
17X-RAY DIFFRACTION17E1 - 9
18X-RAY DIFFRACTION18E10 - 14
19X-RAY DIFFRACTION19F1 - 6
20X-RAY DIFFRACTION20F7 - 14

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