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- PDB-3qku: Mre11 Rad50 binding domain in complex with Rad50 and AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 3qku
TitleMre11 Rad50 binding domain in complex with Rad50 and AMP-PNP
Components
  • DNA double-strand break repair protein mre11
  • DNA double-strand break repair rad50 ATPase
KeywordsREPLICATION / RecA-like fold / coiled-coils / ATPase / exonuclease / endonuclease / ATP binding / DNA binding
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 / ATP hydrolysis 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 / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / : / Mre11 nuclease, N-terminal metallophosphatase domain / Rad50/SbcC-type AAA domain ...Mre11 nuclease, second domain / DNA double-strand break repair protein Mre11, archaea-type / AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / : / Mre11 nuclease, N-terminal metallophosphatase domain / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA double-strand break repair Rad50 ATPase / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWilliams, G.J. / Williams, R.S. / Arvai, A. / Moncalian, G. / Tainer, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.
Authors: Williams, G.J. / Williams, R.S. / Williams, J.S. / Moncalian, G. / Arvai, A.S. / Limbo, O. / Guenther, G. / Sildas, S. / Hammel, M. / Russell, P. / Tainer, J.A.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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_ref_seq_dif / 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_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.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_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

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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 rad50 ATPase
B: DNA double-strand break repair rad50 ATPase
C: DNA double-strand break repair protein mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2517
Polymers86,1903
Non-polymers1,0614
Water00
1
A: DNA double-strand break repair rad50 ATPase
C: DNA double-strand break repair protein mre11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6574
Polymers45,1262
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-27 kcal/mol
Surface area19130 Å2
MethodPISA
2
B: DNA double-strand break repair rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5943
Polymers41,0631
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.398, 177.398, 130.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DNA double-strand break repair rad50 ATPase / Rad50 ABC-ATPase


Mass: 41063.473 Da / Num. of mol.: 2 / Fragment: UNP residues 1-187, 716-882
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rad50, PF1167 / Production host: Escherichia coli (E. coli)
References: UniProt: P58301, Hydrolases; Acting on acid anhydrides
#2: Protein/peptide DNA double-strand break repair protein mre11 / Mre11 Nuclease / pfMre11


Mass: 4062.568 Da / Num. of mol.: 1 / Fragment: Rad50 binding domain (UNP residues 348-381)
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, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Sequence detailsTHE RAD50 ABC-ATPASE CONSTRUCT CONSISTS OF UNP RESIDUES 1-187 AND 716-882 CONNECTED BY AN ...THE RAD50 ABC-ATPASE CONSTRUCT CONSISTS OF UNP RESIDUES 1-187 AND 716-882 CONNECTED BY AN ENGINEERED LINKER (GGSGG)

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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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 200-300 mM lithium sulfate, 12-13% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007
RadiationMonochromator: Kohzu Dual Double Crystal Monochromator (DDCM) Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 3.3→153.6 Å / Num. all: 18722 / Num. obs: 18667 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 35.7
Reflection shellResolution: 3.301→3.387 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 99.41

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US8

1us8


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 32.231 / SU ML: 0.511 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.584 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30838 952 5.1 %RANDOM
Rwork0.25801 ---
obs0.26052 17714 99.79 %-
all-17751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.25 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 134.928 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0.73 Å20 Å2
2---1.46 Å20 Å2
3---2.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 64 0 5626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9967698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85923.665251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.763151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.061544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024131
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22836
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23883
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2981.53539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.69325536
X-RAY DIFFRACTIONr_scbond_it12.95732464
X-RAY DIFFRACTIONr_scangle_it19.4264.52162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.301→3.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 69 -
Rwork0.374 1274 -
obs--99.41 %

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