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- PDB-4q0z: The catalytic core of Rad2 in complex with DNA substrate (complex III) -

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Basic information

Entry
Database: PDB / ID: 4q0z
TitleThe catalytic core of Rad2 in complex with DNA substrate (complex III)
Components
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
  • DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
  • Rad2p
KeywordsHydrolase/DNA / ba Rossmann-like / DNA repair / TFIIH / 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: 2.398 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: Rad2p
B: Rad2p
C: DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
E: Rad2p
F: Rad2p
G: DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
H: DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,86616
Polymers189,5508
Non-polymers3178
Water14,826823
1
A: Rad2p
B: Rad2p
C: DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9338
Polymers94,7754
Non-polymers1584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-60 kcal/mol
Surface area34790 Å2
MethodPISA
2
E: Rad2p
F: Rad2p
G: DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3')
H: DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9338
Polymers94,7754
Non-polymers1584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-67 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.278, 86.039, 134.440
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABEF

#1: Protein
Rad2p


Mass: 42189.062 Da / Num. of mol.: 4 / Fragment: Rad2 catalytic core
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

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DNA chain , 2 types, 4 molecules CGDH

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


Mass: 5120.307 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3')


Mass: 5276.435 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 831 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% (w/v) PEG 8000, 20% (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 MES/imidazole, ...Details: 10% (w/v) PEG 8000, 20% (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 MES/imidazole, pH 6.5, 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: 2.4→40 Å / Num. all: 92334 / Num. obs: 92066 / % possible obs: 99.71 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.751 / % possible all: 99.5

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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: 4Q0R

4q0r


Resolution: 2.398→34.329 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 4607 5 %
Rwork0.178 --
obs0.1808 92066 99.71 %
all-92334 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→34.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9896 1346 8 823 12073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813230
X-RAY DIFFRACTIONf_angle_d1.12318342
X-RAY DIFFRACTIONf_dihedral_angle_d20.6295032
X-RAY DIFFRACTIONf_chiral_restr0.0682031
X-RAY DIFFRACTIONf_plane_restr0.0051907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3977-2.42490.31500.23942731X-RAY DIFFRACTION95
2.4249-2.45340.33621480.24282957X-RAY DIFFRACTION100
2.4534-2.48340.32331470.2332839X-RAY DIFFRACTION100
2.4834-2.51480.2841540.22472917X-RAY DIFFRACTION100
2.5148-2.54790.29431520.20882911X-RAY DIFFRACTION100
2.5479-2.58280.28461620.21092927X-RAY DIFFRACTION100
2.5828-2.61960.31051520.21262882X-RAY DIFFRACTION100
2.6196-2.65870.25611520.2132907X-RAY DIFFRACTION100
2.6587-2.70030.25721340.20092951X-RAY DIFFRACTION100
2.7003-2.74450.29291800.19522903X-RAY DIFFRACTION100
2.7445-2.79180.26541570.19672882X-RAY DIFFRACTION100
2.7918-2.84260.26611430.19332903X-RAY DIFFRACTION100
2.8426-2.89720.27381530.19512907X-RAY DIFFRACTION100
2.8972-2.95630.26611540.19682934X-RAY DIFFRACTION100
2.9563-3.02060.24621490.19872875X-RAY DIFFRACTION100
3.0206-3.09080.26791500.19932939X-RAY DIFFRACTION100
3.0908-3.1680.26931730.19212908X-RAY DIFFRACTION100
3.168-3.25360.29061520.18722911X-RAY DIFFRACTION100
3.2536-3.34930.24191600.18772905X-RAY DIFFRACTION100
3.3493-3.45730.25431210.18622953X-RAY DIFFRACTION100
3.4573-3.58070.24521520.18042935X-RAY DIFFRACTION100
3.5807-3.72390.20721580.17582891X-RAY DIFFRACTION100
3.7239-3.89320.20251480.15452942X-RAY DIFFRACTION100
3.8932-4.09810.18431490.14812954X-RAY DIFFRACTION100
4.0981-4.35440.21521570.14452906X-RAY DIFFRACTION100
4.3544-4.68990.21351420.13772949X-RAY DIFFRACTION100
4.6899-5.16040.21111610.14562944X-RAY DIFFRACTION100
5.1604-5.90380.21281630.16352945X-RAY DIFFRACTION100
5.9038-7.42580.21641630.1792969X-RAY DIFFRACTION100
7.4258-34.33280.16961710.17032982X-RAY DIFFRACTION98

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