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- PDB-4tug: Crystal structure of MjMre11-DNA2 complex -

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Basic information

Entry
Database: PDB / ID: 4tug
TitleCrystal structure of MjMre11-DNA2 complex
Components
  • DNA (5'-D(P*CP*TP*GP*TP*CP*CP*TP*AP*CP*GP*TP*GP*CP*CP*A)-3')
  • DNA (5'-D(P*GP*CP*AP*CP*GP*TP*AP*GP*GP*AP*CP*AP*GP*C)-3')
  • DNA double-strand break repair protein Mre11
KeywordsDNA binding protein/DNA / Nuclease / DNA binding protein-DNA complex
Function / homology
Function and homology information


DNA exonuclease activity / Y-form DNA binding / DNA end binding / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / DNA binding / identical protein binding
Similarity search - Function
Double Stranded RNA Binding Domain - #600 / : / Mre11 C-terminal Rad50-binding domain / DNA double-strand break repair protein Mre11, archaea-type / : / Mre11 nuclease, N-terminal metallophosphatase domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...Double Stranded RNA Binding Domain - #600 / : / Mre11 C-terminal Rad50-binding domain / DNA double-strand break repair protein Mre11, archaea-type / : / Mre11 nuclease, N-terminal metallophosphatase domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Double Stranded RNA Binding Domain / 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 speciesMethanocaldococcus jannaschii (archaea)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.55 Å
AuthorsSung, S. / Cho, Y.
CitationJournal: Embo J. / Year: 2014
Title: DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA.
Authors: Sung, S. / Li, F. / Park, Y.B. / Kim, J.S. / Kim, A.K. / Song, O.K. / Kim, J. / Che, J. / Lee, S.E. / Cho, Y.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _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
C: DNA double-strand break repair protein Mre11
A: DNA double-strand break repair protein Mre11
B: DNA double-strand break repair protein Mre11
D: DNA double-strand break repair protein Mre11
E: DNA double-strand break repair protein Mre11
F: DNA double-strand break repair protein Mre11
G: DNA (5'-D(P*GP*CP*AP*CP*GP*TP*AP*GP*GP*AP*CP*AP*GP*C)-3')
H: DNA (5'-D(P*CP*TP*GP*TP*CP*CP*TP*AP*CP*GP*TP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,35520
Polymers247,0648
Non-polymers29212
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-146 kcal/mol
Surface area90370 Å2
Unit cell
Length a, b, c (Å)91.530, 185.624, 106.212
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA double-strand break repair protein Mre11


Mass: 39704.672 Da / Num. of mol.: 6 / Fragment: UNP residues 1-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: mre11, MJ1323 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58719
#2: DNA chain DNA (5'-D(P*GP*CP*AP*CP*GP*TP*AP*GP*GP*AP*CP*AP*GP*C)-3')


Mass: 4314.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*GP*TP*CP*CP*TP*AP*CP*GP*TP*GP*CP*CP*A)-3')


Mass: 4520.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 41919 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 13.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 3.55→42.422 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1996 5.05 %
Rwork0.1842 --
obs0.1868 39540 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→42.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 592 12 20 16104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916516
X-RAY DIFFRACTIONf_angle_d1.16322291
X-RAY DIFFRACTIONf_dihedral_angle_d17.6016424
X-RAY DIFFRACTIONf_chiral_restr0.0772357
X-RAY DIFFRACTIONf_plane_restr0.0042751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.64340.3431680.23111531X-RAY DIFFRACTION53
3.6434-3.74180.26171230.22072093X-RAY DIFFRACTION75
3.7418-3.85190.26341460.19492651X-RAY DIFFRACTION93
3.8519-3.97610.23821550.19322781X-RAY DIFFRACTION98
3.9761-4.11810.25591220.17652838X-RAY DIFFRACTION99
4.1181-4.28280.22951500.16892825X-RAY DIFFRACTION100
4.2828-4.47760.22731470.16062831X-RAY DIFFRACTION100
4.4776-4.71330.2451560.16012842X-RAY DIFFRACTION100
4.7133-5.00820.21961400.15772867X-RAY DIFFRACTION100
5.0082-5.39420.19211790.16032829X-RAY DIFFRACTION100
5.3942-5.93570.23841530.17982845X-RAY DIFFRACTION100
5.9357-6.79160.24361390.20382868X-RAY DIFFRACTION100
6.7916-8.54520.25611530.20422877X-RAY DIFFRACTION100
8.5452-42.42470.21981650.19932866X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6192-0.8702-0.87323.56631.10522.90660.2585-0.4573-0.66860.82710.1494-0.06950.3918-0.2717-0.11520.90450.1108-0.02211.0369-0.07670.886146.905417.576735.9608
23.93240.95691.07422.09-0.33053.2102-0.08780.34120.0977-0.177-0.07150.2768-0.2734-0.4631-0.0450.80280.2878-0.08550.9614-0.16840.740542.610424.565122.8238
30.2798-0.5044-0.72770.6210.7554.1028-0.21240.2508-0.4004-0.04270.00420.17680.1393-0.4545-0.02181.0629-0.02180.01371.1777-0.00930.988732.2519.303151.3223
43.2987-0.97380.47050.99121.36253.97170.2678-0.05320.41050.0381-0.1592-0.0065-0.37670.1418-0.05930.8051-0.1482-0.0640.93890.13490.958339.306843.359183.5737
52.8961-0.0523-0.10142.16871.23882.67490.01020.18170.0199-0.10950.1608-0.472-0.0060.72-0.0320.7824-0.07920.06680.9170.10940.872941.650937.727177.8813
60.5699-0.1633-0.69361.4241-0.47643.1543-0.3862-0.01180.27140.3490.2208-0.2909-0.46220.61940.05690.9724-0.1166-0.09270.99860.0170.92342.940542.0129107.18
73.4770.26050.16721.02241.08323.46520.31760.22380.42450.393-0.4493-0.19530.4210.01920.04880.6978-0.14280.07840.9854-0.1430.96326.007228.452974.2776
82.4028-0.2602-0.26612.02950.69863.4493-0.00840.0165-0.07250.0593-0.1780.4119-0.13-0.9740.09430.73390.0035-0.04921.06880.02060.78481.261337.367378.213
94.14520.74580.5942.2070.37244.62290.38670.0721-0.97750.7204-0.63480.86660.1318-1.2373-0.08691.11480.0119-0.06011.6362-0.30511.6203-5.670127.054570.5833
101.5262-0.5099-0.45532.11950.27341.14040.13180.0446-0.9133-0.056-0.06980.23851.2212-0.6894-0.09891.8942-0.4276-0.14881.1476-0.13391.5395.25924.638872.1044
116.397-2.4402-0.13165.12420.60034.11970.26120.8565-0.0252-0.5372-0.38920.235-0.24950.8112-0.17780.8711-0.0604-0.11161.2453-0.0890.970178.980733.159432.7592
123.19220.28151.55181.989-0.40633.73980.10430.1782-0.0131-0.16690.0782-0.29220.34550.4525-0.13340.90990.1515-0.05221.0127-0.13890.754175.685924.776733.1998
136.8068-3.5303-3.07473.65875.47669.7650.3841-1.4339-0.7110.8528-0.2068-0.33850.39120.2844-0.17141.20330.0093-0.25651.24170.00381.064983.415920.349454.5105
142.69930.63680.4031.4199-0.4343.98160.06720.32770.00870.2134-0.2582-0.5103-0.34511.2212-0.08980.85660.0135-0.1251.2901-0.02310.918587.880131.979943.605
151.63041.1060.37790.86620.47212.6041-0.29550.92471.0662-0.3417-0.1354-0.6762-0.18680.8706-0.16641.1088-0.0713-0.03261.47680.10531.262189.760837.982531.4951
163.97490.01940.10880.6386-1.13992.04170.06480.42280.09930.3576-0.1758-0.184-1.1520.6259-0.1671.6471-0.0531-0.13771.65710.17671.91883.035160.926825.0958
170.0978-0.2836-0.06072.2540.58990.14690.74890.32231.38980.1105-0.00090.1435-0.8233-0.4103-0.0222.4098-0.027-0.15291.50490.15971.9772.98163.999231.3165
183.5716-0.5183-0.79921.147-0.84953.03240.7116-0.6220.11150.2491-0.20310.8686-0.1361-0.06910.02281.1465-0.20330.22090.90460.00731.48586.975577.1891102.3534
192.9530.8302-0.27293.4652-1.90841.47110.1319-0.09360.99350.4051-0.08290.8288-0.42340.0606-0.00871.1006-0.1990.25020.737-0.1041.600292.366790.085997.4782
203.4604-1.65630.05135.32460.46373.12970.1414-0.15330.50340.43030.01710.4407-0.1690.489-0.16481.0193-0.15260.07030.7215-0.03240.8315101.671354.181995.633
213.03791.13561.86152.8323-0.26041.7411-0.65530.00582.7669-0.36740.2380.70160.0462-0.1614-0.02740.7654-0.225-0.0020.66290.1032.41753.689676.146889.2814
221.59640.08241.181.10660.27680.9105-0.31960.79250.687-0.3617-0.10510.2986-0.5771-0.24580.13531.60780.2364-0.10431.14310.43162.366444.587484.481779.2814
230.03510.0314-0.06250.0041-0.030.055-0.09090.1864-0.0495-0.4249-0.1579-0.0639-0.1480.24650.05343.2227-0.2595-0.03672.33740.632.126258.046689.366655.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 39 )
2X-RAY DIFFRACTION2chain 'C' and (resid 40 through 227 )
3X-RAY DIFFRACTION3chain 'C' and (resid 228 through 312 )
4X-RAY DIFFRACTION4chain 'A' and (resid -3 through 18 )
5X-RAY DIFFRACTION5chain 'A' and (resid 19 through 227 )
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 313 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 18 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 211 through 235 )
10X-RAY DIFFRACTION10chain 'B' and (resid 236 through 306 )
11X-RAY DIFFRACTION11chain 'D' and (resid 0 through 18 )
12X-RAY DIFFRACTION12chain 'D' and (resid 19 through 129 )
13X-RAY DIFFRACTION13chain 'D' and (resid 130 through 147 )
14X-RAY DIFFRACTION14chain 'D' and (resid 148 through 219 )
15X-RAY DIFFRACTION15chain 'D' and (resid 220 through 256 )
16X-RAY DIFFRACTION16chain 'D' and (resid 257 through 274 )
17X-RAY DIFFRACTION17chain 'D' and (resid 275 through 306 )
18X-RAY DIFFRACTION18chain 'E' and (resid -2 through 39 )
19X-RAY DIFFRACTION19chain 'E' and (resid 40 through 244 )
20X-RAY DIFFRACTION20chain 'E' and (resid 245 through 311 )
21X-RAY DIFFRACTION21chain 'F' and (resid -1 through 227 )
22X-RAY DIFFRACTION22chain 'F' and (resid 228 through 256 )
23X-RAY DIFFRACTION23chain 'F' and (resid 257 through 303 )

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