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- PDB-4q10: The catalytic core of Rad2 in complex with DNA substrate (complex IV) -

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Basic information

Entry
Database: PDB / ID: 4q10
TitleThe catalytic core of Rad2 in complex with DNA substrate (complex IV)
Components
  • DNA (5'-D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP*T)-3')
  • DNA (5'-D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP*T)-3')
  • DNA repair protein RAD2
KeywordsHydrolase/DNA / ba Rossmann-like / DNA repair / TFIIH / nucleus / Hydrolase-DNA complex
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / nucleotide-excision repair factor 3 complex / Dual incision in TC-NER / DNA endonuclease activity / nucleotide-excision repair / single-stranded DNA binding / transcription by RNA polymerase II / Hydrolases; Acting on ester bonds / metal ion binding / nucleus
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA repair protein RAD2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMietus, M. / Nowak, E. / Jaciuk, M. / Kustosz, P. / Nowotny, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.
Authors: Mietus, M. / Nowak, E. / Jaciuk, M. / Kustosz, P. / Studnicka, J. / Nowotny, M.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 RAD2
B: DNA repair protein RAD2
C: DNA (5'-D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP*T)-3')
D: DNA (5'-D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5848
Polymers98,4254
Non-polymers1584
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-61 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.680, 97.958, 112.038
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA repair protein RAD2


Mass: 42189.062 Da / Num. of mol.: 2
Fragment: enzyme catalytic core, unp residues 2-111, unp residues 732-986
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RAD2, YGR258C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosseta
References: UniProt: P07276, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP*T)-3')


Mass: 6945.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide
#3: DNA chain DNA (5'-D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP*T)-3')


Mass: 7101.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide

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Non-polymers , 3 types, 130 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH ...Details: 8% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8944 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8944 Å / Relative weight: 1
ReflectionResolution: 2.7→111.3 Å / Num. all: 29227 / Num. obs: 27918 / % possible obs: 95.52 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4Q0R

4q0r


Resolution: 2.7→43.133 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 1414 5.06 %random
Rwork0.2316 ---
obs0.2344 27918 95.52 %-
all-29227 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→43.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 663 4 126 5463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076284
X-RAY DIFFRACTIONf_angle_d1.0068750
X-RAY DIFFRACTIONf_dihedral_angle_d22.6552349
X-RAY DIFFRACTIONf_chiral_restr0.065983
X-RAY DIFFRACTIONf_plane_restr0.005896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79650.33961460.27992770X-RAY DIFFRACTION100
2.7965-2.90850.29041500.25292755X-RAY DIFFRACTION100
2.9085-3.04080.34511390.24852769X-RAY DIFFRACTION100
3.0408-3.20110.34571310.24422745X-RAY DIFFRACTION100
3.2011-3.40160.28051300.26482773X-RAY DIFFRACTION100
3.4016-3.66410.38771040.29832166X-RAY DIFFRACTION77
3.6641-4.03260.35731390.26682227X-RAY DIFFRACTION82
4.0326-4.61550.23981730.20022743X-RAY DIFFRACTION100
4.6155-5.81280.22891470.20012778X-RAY DIFFRACTION100
5.8128-43.13880.24971550.19922778X-RAY DIFFRACTION98

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