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- PDB-5dac: ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex w... -

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Basic information

Entry
Database: PDB / ID: 5dac
TitleATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA
Components
  • DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
  • Putative uncharacterized protein,Putative uncharacterized protein
KeywordsHYDROLASE / ATPase / ATPyS bound
Function / homology
Function and homology information


Mre11 complex / Hydrolases; Acting on acid anhydrides / telomere maintenance / guanyl-nucleotide exchange factor activity / double-strand break repair / chromosome / double-stranded DNA binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
DNA repair protein Rad50, eukaryotes / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA repair protein RAD50
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsSeifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.-P.
CitationJournal: Embo J. / Year: 2016
Title: Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50.
Authors: Seifert, F.U. / Lammens, K. / Stoehr, G. / Kessler, B. / Hopfner, K.P.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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.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.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_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
A: Putative uncharacterized protein,Putative uncharacterized protein
B: Putative uncharacterized protein,Putative uncharacterized protein
C: DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
D: DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,40210
Polymers109,9014
Non-polymers1,5026
Water1,874104
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-46 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.312, 97.078, 115.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative uncharacterized protein,Putative uncharacterized protein


Mass: 50357.375 Da / Num. of mol.: 2 / Mutation: E1238Q,E1238Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0073630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHW7

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 4292.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 4893.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 110 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.25 M potassium acetate, 42% (v/v) pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9716 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36106 / % possible obs: 99.5 % / Redundancy: 12.8 % / Rsym value: 0.2 / Net I/σ(I): 11.96
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 1.33 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5da9

5da9


Resolution: 2.503→49.477 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1805 5 %
Rwork0.2103 --
obs0.2121 36099 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→49.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 615 90 104 7640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087699
X-RAY DIFFRACTIONf_angle_d1.19210510
X-RAY DIFFRACTIONf_dihedral_angle_d18.2942989
X-RAY DIFFRACTIONf_chiral_restr0.051207
X-RAY DIFFRACTIONf_plane_restr0.0051235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.57070.36331280.32752423X-RAY DIFFRACTION94
2.5707-2.64630.33361370.29962610X-RAY DIFFRACTION100
2.6463-2.73170.29961380.27472613X-RAY DIFFRACTION100
2.7317-2.82940.28251370.262605X-RAY DIFFRACTION100
2.8294-2.94260.27551400.26642659X-RAY DIFFRACTION100
2.9426-3.07650.30341370.25832602X-RAY DIFFRACTION100
3.0765-3.23870.29931380.27222620X-RAY DIFFRACTION100
3.2387-3.44160.32051390.24722640X-RAY DIFFRACTION100
3.4416-3.70720.28171400.21752663X-RAY DIFFRACTION100
3.7072-4.08010.23671390.20332651X-RAY DIFFRACTION100
4.0801-4.67020.21071410.16192671X-RAY DIFFRACTION100
4.6702-5.88240.20661420.17972708X-RAY DIFFRACTION100
5.8824-49.48640.18741490.1742829X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 39.4474 Å / Origin y: 38.8463 Å / Origin z: 49.1344 Å
111213212223313233
T0.1631 Å20.0075 Å20.0472 Å2-0.4339 Å20.0403 Å2--0.4212 Å2
L0.4808 °20.1647 °20.3134 °2-0.5783 °20.0383 °2--0.3465 °2
S-0.0517 Å °-0.0446 Å °-0.1483 Å °-0.0231 Å °0.0048 Å °-0.1794 Å °0.0526 Å °0.0427 Å °0.0403 Å °
Refinement TLS groupSelection details: all

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