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- PDB-3dsd: Crystal structure of P. furiosus Mre11-H85S bound to a branched D... -

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Basic information

Entry
Database: PDB / ID: 3dsd
TitleCrystal structure of P. furiosus Mre11-H85S bound to a branched DNA and manganese
Components
  • DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DGP*DAP*DTP*DA)-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 exonuclease activity / 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 / 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 ...DNA double-strand break repair nuclease / 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: 2.2 Å
AuthorsWilliams, R.S. / Moiani, D. / 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: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 double-strand break repair protein mre11
C: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DGP*DAP*DTP*DA)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9537
Polymers89,7333
Non-polymers2204
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-41 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.157, 88.128, 137.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40869.590 Da / Num. of mol.: 2 / Fragment: pfMre11 Nuclease domain / Mutation: H85S
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(*DCP*DGP*DCP*DGP*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP*DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DGP*DAP*DTP*DA)-3')


Mass: 7994.150 Da / Num. of mol.: 1 / Fragment: Branched DNA hairpin / Source method: obtained synthetically
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% PEG 200, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 20011
2HEPES11
3PEG 20012
4HEPES12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1159 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 47737 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.1

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Processing

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

1ii7


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.604 / SU ML: 0.144 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24606 2402 5 %RANDOM
Rwork0.19955 ---
all0.20196 47737 --
obs0.20196 45184 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2---1.68 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 473 4 300 6277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.392.0668421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37423.451284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5321542
X-RAY DIFFRACTIONr_chiral_restr0.0930.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.32614
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.54114
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5587
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.382
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.538
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9331.53395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55325338
X-RAY DIFFRACTIONr_scbond_it2.00333306
X-RAY DIFFRACTIONr_scangle_it3.1524.53083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 148 -
Rwork0.24 3219 -
obs--95.19 %

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