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- PDB-4ep5: Thermus thermophilus RuvC structure -

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Basic information

Entry
Database: PDB / ID: 4ep5
TitleThermus thermophilus RuvC structure
ComponentsCrossover junction endodeoxyribonuclease RuvC
KeywordsHYDROLASE / resolvase
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Crossover junction endodeoxyribonuclease RuvC / Crossover junction endodeoxyribonuclease RuvC / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsChen, L. / Shi, K. / Yin, Z.Q. / Aihara, H.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.
Authors: Chen, L. / Shi, K. / Yin, Z. / Aihara, H.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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_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: Crossover junction endodeoxyribonuclease RuvC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2576
Polymers17,7811
Non-polymers4765
Water36020
1
A: Crossover junction endodeoxyribonuclease RuvC
hetero molecules

A: Crossover junction endodeoxyribonuclease RuvC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51412
Polymers35,5622
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area3450 Å2
ΔGint-125 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.183, 60.019, 135.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-314-

HOH

31A-318-

HOH

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Components

#1: Protein Crossover junction endodeoxyribonuclease RuvC / Holliday junction nuclease RuvC / Holliday junction resolvase RuvC


Mass: 17780.820 Da / Num. of mol.: 1 / Mutation: D146N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruvC, TTHA1090 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SJC4, crossover junction endodeoxyribonuclease
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 293 K / pH: 4.2
Details: PEG400, Li2SO4, and sodium acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 8463 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 6.5
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.698 / % possible all: 0.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1005)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→36.13 Å / SU ML: 0.23 / σ(F): 1.37 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 844 10 %
Rwork0.208 --
obs0.213 8444 92.9 %
all-8444 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.3775 Å2-0 Å20 Å2
2--26.8988 Å2-0 Å2
3----18.5213 Å2
Refinement stepCycle: LAST / Resolution: 2.08→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 26 20 1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061210
X-RAY DIFFRACTIONf_angle_d0.9741640
X-RAY DIFFRACTIONf_dihedral_angle_d14.88432
X-RAY DIFFRACTIONf_chiral_restr0.06186
X-RAY DIFFRACTIONf_plane_restr0.004206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0747-2.20470.31611070.2548954X-RAY DIFFRACTION72
2.2047-2.37490.33321260.2281150X-RAY DIFFRACTION86
2.3749-2.61380.2221480.20371322X-RAY DIFFRACTION98
2.6138-2.99190.19681500.19981353X-RAY DIFFRACTION100
2.9919-3.76880.251510.20251368X-RAY DIFFRACTION100
3.7688-36.13450.27781620.20491453X-RAY DIFFRACTION100
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)
12.6679-0.9745-1.70225.7098-1.08311.63530.3361-0.10520.0070.26310.2264-0.43260.02240.1848-0.54610.1689-0.01210.0410.7557-0.06010.43995.38172.85119.471
25.8978-3.5081-2.6537.0492-3.41346.21080.10380.9119-0.3848-0.03710.0737-0.157-1.13870.28-0.10940.2209-0.0180.04140.3793-0.02110.20332.98126.132718.0434
33.49330.4731-3.18456.0089-2.65783.7291-0.39251.42310.1238-1.0546-0.44261.55550.8459-1.11910.85250.4865-0.0952-0.12221.0817-0.09640.6761.5416-4.26950.7334
42.7748-2.3067-2.16784.04453.17918.65220.44920.8704-0.1808-0.6048-0.69330.3174-0.7176-0.96740.20710.38870.0086-0.04720.69960.02630.3273-0.03637.70913.8409
58.74235.27556.83363.3714.7427.4334-1.43770.7786-0.2265-0.72311.2487-0.4114-1.13430.90050.01720.5418-0.0849-0.05280.68130.03990.38865.532714.654236.0388
69.61933.7673-2.12052.18440.53336.46270.0489-0.26060.96270.3166-0.26790.3093-0.25650.31930.17020.23910.0093-0.04020.58590.04770.4071-0.5017.181930.5053
78.41190.6459-0.99874.0372.97068.9815-0.4597-1.17771.10530.4349-0.02751.260.5197-1.46530.35820.3013-0.0498-0.05320.9922-0.02010.4937-8.05972.032920.1202
84.4215-0.0305-1.66122.13-0.36391.8028-0.24950.1043-0.67910.08640.08890.53830.1651-0.15570.0367-0.30190.04490.12690.76540.0310.38640.6686-4.202217.8114
95.2772-4.91561.73826.08670.66144.0265-0.0578-1.097-0.79161.01620.4202-1.57950.01830.8614-0.23110.3379-0.0681-0.16291.33960.45350.895113.7385-0.565921.6328
105.0229-2.5835-4.86851.74242.35434.77310.0971-0.69520.45870.39220.2313-0.1464-0.26180.9041-0.24540.423-0.13170.00871.38570.19040.489512.17163.448234.544
111.214-0.343-0.60721.43911.45163.8875-0.3854-0.1713-0.50560.0504-0.03930.40880.4422-0.01830.3430.2186-0.02540.05510.54060.05540.41712.9573-4.43824.6439
123.1147-2.12884.95597.2654-1.83978.3258-0.1587-0.1842-1.0211-0.02350.4937-0.38250.64440.7978-0.2210.23120.06520.03210.8215-0.00040.472416.9152-2.7799.8791
139.3026-5.1021-0.07464.0431-1.24351.33440.0561-0.21190.9984-0.17680.2768-0.0759-0.6203-0.16130.1940.2073-0.06130.00630.9893-0.15340.634720.49653.13318.897
142.81684.27021.58776.56531.7938.2483-0.21661.64940.4398-1.12070.3121-0.3195-0.55920.5533-0.05380.44110.10440.11980.72480.11280.38479.07236.8924.1833
159.63131.10.58764.8057-5.25399.13640.3926-0.80770.72490.1905-0.06470.8543-2.53670.59320.02040.8040.04110.00380.3527-0.0770.53518.153713.583611.023
167.51192.4446-1.11914.6654-0.32913.47180.0537-0.1459-0.8878-0.23970.1202-1.07080.00260.5333-0.14350.17370.0272-0.0110.6841-0.04320.29888.0814-0.692312.1809
176.0686-1.1252-0.35986.09675.32969.0843-0.76760.2932-1.4950.42410.27910.2462.36871.87430.56180.67170.25010.18890.7575-0.04721.04937.918-11.603912.7308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:11)
2X-RAY DIFFRACTION2(chain A and resid 12:19)
3X-RAY DIFFRACTION3(chain A and resid 20:26)
4X-RAY DIFFRACTION4(chain A and resid 27:37)
5X-RAY DIFFRACTION5(chain A and resid 38:45)
6X-RAY DIFFRACTION6(chain A and resid 46:56)
7X-RAY DIFFRACTION7(chain A and resid 57:63)
8X-RAY DIFFRACTION8(chain A and resid 64:69)
9X-RAY DIFFRACTION9(chain A and resid 70:80)
10X-RAY DIFFRACTION10(chain A and resid 81:86)
11X-RAY DIFFRACTION11(chain A and resid 87:107)
12X-RAY DIFFRACTION12(chain A and resid 108:116)
13X-RAY DIFFRACTION13(chain A and resid 117:125)
14X-RAY DIFFRACTION14(chain A and resid 126:134)
15X-RAY DIFFRACTION15(chain A and resid 135:143)
16X-RAY DIFFRACTION16(chain A and resid 144:157)
17X-RAY DIFFRACTION17(chain A and resid 158:166)

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