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- PDB-1p59: Structure of a non-covalent Endonuclease III-DNA Complex -

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Basic information

Entry
Database: PDB / ID: 1p59
TitleStructure of a non-covalent Endonuclease III-DNA Complex
Components
  • 5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3'
  • 5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3'
  • Endonuclease III
KeywordsHYDROLASE/DNA / DNA REPAIR / DNA GLYCOSYLASE / [4FE-4S] CLUSTER / IRON-SULFUR CLUSTER / HYDROLASE-DNA COMPLEX
Function / homologyHelix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha / IRON/SULFUR CLUSTER / DNA / DNA (> 10)
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsFromme, J.C. / Verdine, G.L.
CitationJournal: Embo J. / Year: 2003
Title: Structure of a Trapped Endonuclease III-DNA Covalent Intermediate
Authors: Fromme, J.C. / Verdine, G.L.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHORS INFORMED THAT THE PROTEIN SEQUENCE HAS NOT YET BEEN PUBLISHED. RESIDUES GLY -2, ...SEQUENCE AUTHORS INFORMED THAT THE PROTEIN SEQUENCE HAS NOT YET BEEN PUBLISHED. RESIDUES GLY -2, SER -1 AND HIS 0 ARE CLONING ARTIFACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3'
C: 5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3'
A: Endonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5455
Polymers33,1713
Non-polymers3752
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.321, 105.896, 41.518
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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DNA chain , 2 types, 2 molecules BC

#1: DNA chain 5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3'


Mass: 3519.119 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3'


Mass: 3414.813 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Endonuclease III /


Mass: 26236.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: NTH / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(C41)

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Non-polymers , 3 types, 33 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, TRIS, BME, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2TRIS11
3BME11
4PEG 800012
5TRIS12
6BME12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH8.5
220-25 %(w/v)PEG80001reservoir
35 mMbeta-mercaptoethanol1reservoir
41
51
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2002
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 19576 / Num. obs: 17421 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1997 / % possible all: 83.1
Reflection
*PLUS
Redundancy: 3.3 %
Reflection shell
*PLUS
% possible obs: 83.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1ORN

1orn


Resolution: 2.5→29.31 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 854279.88 / Data cutoff high rms absF: 854279.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1599 9.4 %RANDOM
Rwork0.214 ---
obs0.214 17052 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.0823 Å2 / ksol: 0.317717 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2---6.18 Å20 Å2
3---1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 417 9 31 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it3.982
X-RAY DIFFRACTIONc_scangle_it4.622.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 130 8.3 %
Rwork0.295 1432 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5FS4.PARAMFS4.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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