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- PDB-4q0w: he catalytic core of Rad2 in complex with DNA substrate (complex II) -

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Basic information

Entry
Database: PDB / ID: 4q0w
Titlehe catalytic core of Rad2 in complex with DNA substrate (complex II)
Components
  • DNA (5'-D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3')
  • DNA (5'-D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*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 / Hydrolases; Acting on ester bonds / transcription by RNA polymerase II / 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: 2.1 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 1.3Oct 29, 2014Group: Structure summary
Revision 1.4Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Sep 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_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_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.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*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3')
D: DNA (5'-D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5328
Polymers95,3734
Non-polymers1584
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-67 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.641, 76.813, 108.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: Rad2
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*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3')


Mass: 5408.500 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3')


Mass: 5586.625 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 571 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.: 567 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 9% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 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. ...Details: 9% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 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: RAYONIX MX-225 / 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: 2.14→40 Å / Num. all: 62290 / Num. obs: 62159 / % possible obs: 99.79 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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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: 2.1→30.386 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3152 5.07 %random
Rwork0.1834 ---
obs0.1857 62159 99.79 %-
all-62290 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→30.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 616 4 567 6098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075772
X-RAY DIFFRACTIONf_angle_d1.0537946
X-RAY DIFFRACTIONf_dihedral_angle_d17.7442183
X-RAY DIFFRACTIONf_chiral_restr0.064876
X-RAY DIFFRACTIONf_plane_restr0.004921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13130.30941430.22982519X-RAY DIFFRACTION99
2.1313-2.16460.26831240.21882513X-RAY DIFFRACTION99
2.1646-2.20010.29091380.22072515X-RAY DIFFRACTION100
2.2001-2.2380.28941330.22992534X-RAY DIFFRACTION100
2.238-2.27870.26181300.21962528X-RAY DIFFRACTION100
2.2787-2.32250.2851510.21122536X-RAY DIFFRACTION100
2.3225-2.36990.26021200.20042530X-RAY DIFFRACTION100
2.3699-2.42140.2431270.19552538X-RAY DIFFRACTION100
2.4214-2.47770.27311320.19392574X-RAY DIFFRACTION100
2.4777-2.53970.22861290.19652540X-RAY DIFFRACTION100
2.5397-2.60830.26811370.19782546X-RAY DIFFRACTION100
2.6083-2.6850.25521340.19042553X-RAY DIFFRACTION100
2.685-2.77160.24481360.20242575X-RAY DIFFRACTION100
2.7716-2.87060.2451260.1992566X-RAY DIFFRACTION100
2.8706-2.98550.27091590.20092535X-RAY DIFFRACTION100
2.9855-3.12120.24411370.20542558X-RAY DIFFRACTION100
3.1212-3.28560.23581300.19512582X-RAY DIFFRACTION100
3.2856-3.49120.23851370.18852603X-RAY DIFFRACTION100
3.4912-3.76030.23481580.17442543X-RAY DIFFRACTION100
3.7603-4.13780.17931480.14952585X-RAY DIFFRACTION100
4.1378-4.73460.1721290.13492634X-RAY DIFFRACTION100
4.7346-5.95780.20331460.16752650X-RAY DIFFRACTION100
5.9578-30.38910.22061480.18972750X-RAY DIFFRACTION100

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