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- PDB-3dsc: Crystal structure of P. furiosus Mre11 DNA synaptic complex -

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Basic information

Entry
Database: PDB / ID: 3dsc
TitleCrystal structure of P. furiosus Mre11 DNA synaptic complex
Components
  • DNA (5'-D(P*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DAP*DC)-3')
  • DNA double-strand break repair protein mre11
KeywordsHydrolase/DNA / Protein-DNA complex / Double Helix / Nuclease / DNA damage / DNA repair / Endonuclease / Exonuclease / Hydrolase / Manganese / Metal-binding / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


DNA end binding / Y-form DNA binding / DNA double-strand break processing / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding
Similarity search - Function
DNA double-strand break repair nuclease / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / : / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...DNA double-strand break repair nuclease / Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / : / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWilliams, R.S. / Moncalian, G. / Shin, D.S. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair.
Authors: Williams, R.S. / Moncalian, G. / Williams, J.S. / Yamada, Y. / Limbo, O. / Shin, D.S. / Groocock, L.M. / Cahill, D. / Hitomi, C. / Guenther, G. / Moiani, D. / Carney, J.P. / Russell, P. / Tainer, J.A.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Feb 26, 2020Group: Advisory / Data collection / Database references
Category: pdbx_unobs_or_zero_occ_atoms / reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA double-strand break repair protein mre11
B: DNA (5'-D(P*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DAP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)47,0212
Polymers47,0212
Non-polymers00
Water1,13563
1
A: DNA double-strand break repair protein mre11
B: DNA (5'-D(P*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DAP*DC)-3')

A: DNA double-strand break repair protein mre11
B: DNA (5'-D(P*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DAP*DC)-3')


Theoretical massNumber of molelcules
Total (without water)94,0414
Polymers94,0414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area18580 Å2
Unit cell
Length a, b, c (Å)98.477, 106.071, 76.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21B-21-

HOH

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Components

#1: Protein DNA double-strand break repair protein mre11 / pfMre11


Mass: 40920.660 Da / Num. of mol.: 1 / Fragment: pfMre11 Nuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: mre11, PF1166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N9
#2: DNA chain DNA (5'-D(P*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DAP*DC)-3')


Mass: 6099.952 Da / Num. of mol.: 1 / Fragment: 3' overhang DNA hairpin / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 1000, 0.1 M Tris-HCl, 0.2 M MgCl2, 0.2 M 1,6 hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 100011
2Tris11
3MgCl211
41,6 hexanediol11
5PEG 100012
6Tris12
7MgCl212
81,6 hexanediol12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 10769 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1II7

1ii7


Resolution: 2.7→19.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / SU B: 32.169 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27804 545 5.3 %RANDOM
Rwork0.22756 ---
all0.23034 10769 --
obs0.23034 9708 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.368 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--4.77 Å20 Å2
3----3.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 348 0 63 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9832.1044394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48123.521142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05915504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022329
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1460.31321
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.52109
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.5166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.372
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.19921696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35432668
X-RAY DIFFRACTIONr_scbond_it0.0621817
X-RAY DIFFRACTIONr_scangle_it0.09931726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 29 -
Rwork0.298 569 -
obs--86.54 %
Refinement TLS params.Method: refined / Origin x: 21.9472 Å / Origin y: 6.5159 Å / Origin z: 18.1059 Å
111213212223313233
T-0.0888 Å2-0.0087 Å2-0.017 Å2-0.0081 Å2-0.0032 Å2---0.04 Å2
L3.0199 °2-0.4391 °20.175 °2-2.8192 °20.0457 °2--2.3164 °2
S0.0534 Å °0.1333 Å °0.2129 Å °-0.1842 Å °0.0151 Å °0.3944 Å °-0.1121 Å °-0.3717 Å °-0.0684 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB1 - 3331 - 333
2X-RAY DIFFRACTION1BA1 - 191 - 19

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