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- PDB-4w9m: AMPPNP bound Rad50 in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 4w9m
TitleAMPPNP bound Rad50 in complex with dsDNA
Components
  • DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')
  • Exonuclease, putative
  • Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
KeywordsHYDROLASE / ATPase / DNA AMPPNP bound
Function / homology
Function and homology information


DNA exonuclease activity / Hydrolases; Acting on acid anhydrides / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity ...DNA exonuclease activity / Hydrolases; Acting on acid anhydrides / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Helix hairpin bin / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Nuclease SbcCD subunit D / SbcC/RAD50-like, Walker B motif / Mre11 nuclease, N-terminal metallophosphatase domain / Helix hairpin bin domain superfamily / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type ...Helix hairpin bin / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Nuclease SbcCD subunit D / SbcC/RAD50-like, Walker B motif / Mre11 nuclease, N-terminal metallophosphatase domain / Helix hairpin bin domain superfamily / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA double-strand break repair protein Mre11 / DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsRojowska, A. / Lammens, K.
CitationJournal: Embo J. / Year: 2014
Title: Structure of the Rad50 DNA double-strand break repair protein in complex with DNA.
Authors: Rojowska, A. / Lammens, K. / Seifert, F.U. / Direnberger, C. / Feldmann, H. / Hopfner, K.P.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Other
Revision 2.0Oct 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')
A: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')
C: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
D: Exonuclease, putative
E: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
F: Exonuclease, putative
Z: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')
I: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
J: Exonuclease, putative
K: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
L: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38320
Polymers201,26112
Non-polymers2,1228
Water4,810267
1
Y: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')
A: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')
C: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
D: Exonuclease, putative
E: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
F: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,69110
Polymers100,6306
Non-polymers1,0614
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Z: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')
I: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
J: Exonuclease, putative
K: Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase
L: Exonuclease, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,69110
Polymers100,6306
Non-polymers1,0614
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.713, 96.386, 105.926
Angle α, β, γ (deg.)90.010, 89.220, 81.670
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 4 molecules YZAG

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


Mass: 4610.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3')


Mass: 4570.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Protein/peptide , 2 types, 8 molecules CEIKDFJL

#3: Protein
Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase


Mass: 41073.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: rad50, TM_1636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X1
#4: Protein/peptide
Exonuclease, putative / Metallophosphatase


Mass: 4650.368 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1635, THEMA_06070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X0

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Non-polymers , 3 types, 275 molecules

#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 150 mM D-maleic acid pH 6.5, 21% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 51778 / % possible obs: 93.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.51 Å2 / Net I/σ(I): 9.26

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.685 Å / FOM work R set: 0.743 / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 2573 5 %
Rwork0.2148 48866 -
obs0.2176 51439 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.9 Å2 / Biso mean: 44.37 Å2 / Biso min: 11.64 Å2
Refinement stepCycle: final / Resolution: 2.7→47.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12556 1218 740 267 14781
Biso mean--134.41 30.81 -
Num. residues----1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114232
X-RAY DIFFRACTIONf_angle_d1.33719353
X-RAY DIFFRACTIONf_chiral_restr0.0812154
X-RAY DIFFRACTIONf_plane_restr0.0052253
X-RAY DIFFRACTIONf_dihedral_angle_d19.5475573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.7520.47171420.39722707284995
2.752-2.80820.41251420.31862683282597
2.8082-2.86920.40521430.30942724286796
2.8692-2.9360.40521440.30072725286996
2.936-3.00940.39371400.29742675281596
3.0094-3.09070.36691430.29322711285495
3.0907-3.18170.36831440.27472731287597
3.1817-3.28440.29241440.25842738288297
3.2844-3.40170.2991430.21762711285498
3.4017-3.53790.27641460.20572787293397
3.5379-3.69880.26711420.19242699284197
3.6988-3.89370.25971440.18322730287496
3.8937-4.13760.2011420.18092707284996
4.1376-4.45680.21081430.16372703284696
4.4568-4.90490.19851430.15672724286796
4.9049-5.61370.21971430.18452716285996
5.6137-7.0690.25131410.22442680282195
7.069-47.6920.22931440.18552715285997

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