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- PDB-3ve5: Structure of recombination mediator protein RecR16-196 deletion mutant -

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Basic information

Entry
Database: PDB / ID: 3ve5
TitleStructure of recombination mediator protein RecR16-196 deletion mutant
ComponentsRecombination protein recR
KeywordsRECOMBINATION / HhH domain / Zinc Finger / DNA repair / DNA binding
Function / homology
Function and homology information


DNA recombination / DNA repair / DNA binding / zinc ion binding
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / RecR, C-terminal / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger domain / RecR, helix-hairpin-helix / RecR protein signature. / Toprim domain ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / RecR, C-terminal / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger domain / RecR, helix-hairpin-helix / RecR protein signature. / Toprim domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / TOPRIM / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Toprim domain profile. / TOPRIM domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Recombination protein RecR
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, Q. / Yan, X.X. / Liang, D.C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: RecOR complex including RecR N-N dimer and RecO monomer displays a high affinity for ssDNA
Authors: Tang, Q. / Gao, P. / Liu, Y.P. / Gao, A. / An, X.M. / Liu, S. / Yan, X.X. / Liang, D.C.
History
DepositionJan 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_seq_id / _struct_conn.ptnr1_label_asym_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
D: Recombination protein recR
A: Recombination protein recR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5167
Polymers43,1782
Non-polymers3385
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-20 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.384, 84.753, 72.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Recombination protein recR / RecR Recombinational DNA repair protein


Mass: 21588.881 Da / Num. of mol.: 2 / Fragment: UNP residues 19-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: recR / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RDI4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 14%(w/v) PEG33500, 100mM Mes, 150mM Ammonium Sulfate, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9875 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 13020 / Biso Wilson estimate: 52.53 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VDP

3vdp


Resolution: 2.8→19.933 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8313 / SU ML: 0.32 / σ(F): 0 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 639 4.91 %
Rwork0.194 12381 -
obs0.1958 13020 98 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.955 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 138.83 Å2 / Biso mean: 55.2035 Å2 / Biso min: 13.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.6793 Å2-0 Å2-0 Å2
2--0.6197 Å20 Å2
3---2.0596 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 17 53 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122704
X-RAY DIFFRACTIONf_angle_d1.4583661
X-RAY DIFFRACTIONf_chiral_restr0.087442
X-RAY DIFFRACTIONf_plane_restr0.006473
X-RAY DIFFRACTIONf_dihedral_angle_d16.216974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-3.01560.30371270.2752314244194
3.0156-3.31780.28421340.22012420255498
3.3178-3.7950.25521340.194624882622100
3.795-4.77050.16491140.153725462660100
4.7705-19.93330.2241300.19712613274398
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)
10.18990.1680.48930.18340.441.29480.0555-0.4785-0.0846-0.68190.08720.54510.0874-0.3625-0.16510.5109-0.00370.17870.4370.03720.5377-6.70325.019-65.808
20.73150.43180.80580.6359-0.07651.49240.2939-0.1408-0.4458-0.1864-0.28290.39430.6053-0.23370.05280.1508-0.00450.02160.143-0.0650.15332.15614.021-64.961
30.5625-0.4820.47681.1906-0.3383.61730.0310.32830.6185-0.0066-0.2013-0.14610.1478-0.2693-0.04930.14410.05690.04620.30650.21490.28932.62224.012-81.849
40.87730.88350.24780.86260.23640.0890.1735-0.0295-0.2151-0.1225-0.5820.76760.26350.51430.27420.18620.1394-0.02010.84270.31360.4737-3.57923.665-88.073
51.39480.845-0.12372.71790.93760.45960.38520.5627-0.3483-0.5202-0.8682-0.1980.44380.72870.43280.20390.0753-0.00380.80570.03830.1448-1.85622.104-94.495
60.8787-0.308-0.43850.413-0.33290.51920.14051.23650.09790.0598-0.7847-0.378-0.35911.1141-0.1106-0.84351.53012.3388-0.7798-2.9425-5.378-10.28419.931-100.484
72.5416-1.64380.86222.0766-1.69842.7883-0.2235-0.1255-0.0680.80320.3367-0.08840.0807-0.05190.05350.30340.2813-0.07140.52020.04620.151-12.31217.754-84.996
80.9793-0.5139-0.80163.66620.80320.6725-0.40220.0537-0.1155-0.04220.21610.160.19150.18530.01750.6580.2277-0.01550.6575-0.00220.57-12.5619.179-93.055
90.87040.4158-0.17260.9472-0.50980.24760.3345-0.36470.01120.0964-0.3483-0.04460.09151.05240.02230.26810.1389-0.01220.3951-0.01680.0678-16.83325.352-84.008
100.9708-0.63590.24191.0412-0.34330.22390.17470.31920.073-0.1942-0.2884-0.14390.12420.26370.06860.24270.10830.01630.41310.04180.2119-17.9429.002-93.413
113.41860.11671.25091.6246-0.09060.46910.1017-0.9099-0.43640.14780.04-0.13960.2031-0.4181-0.05130.23420.0344-0.0530.2873-0.01720.121-24.64619.14-78.363
120.97950.0273-0.37061.6484-0.90740.84870.77570.62891.60171.54260.03722.2542-0.1141-0.0512-0.1534-2.82322.2827-0.9169-1.52030.4991-0.5112-26.75126.682-90.779
131.01581.2718-0.01581.55230.00520.00590.1227-0.934-0.0093-0.1966-0.05710.05370.17240.20920.22280.5934-0.0930.16240.75830.22890.8007-24.91810.871-82.867
140.7127-1.6455-0.91074.8922.28731.2044-0.1549-1.01450.0997-0.9308-0.08940.57870.81090.32840.16770.61960.162-0.08140.50470.010.64-16.8038.721-83.595
150.0303-0.0189-0.0909-0.00590.03090.03110.31340.26090.32850.03640.3692-0.53770.1247-0.9569-0.11380.63180.0991-0.33030.5889-0.09540.7934-25.57212.743-94.215
160.9218-0.1930.31550.72570.06040.1399-0.10970.2868-0.2079-0.0640.45980.1164-0.2438-0.3876-0.1440.26570.1058-0.0110.38520.04650.2983-4.32621.946-75.152
170.3220.5183-0.09380.9684-0.54550.7063-0.09030.2956-0.01730.4404-0.2662-0.619-0.67220.6552-0.00730.2044-0.09760.0290.24540.2260.4436.023329.9688-72.2141
183.89270.695-0.57331.88550.4483.63430.0619-0.51310.23530.1764-0.2775-0.00830.4222-0.03430.28030.1965-0.0801-0.02810.22240.00620.11082.162917.8005-54.743
190.36580.8551-0.32363.8597-1.45121.02560.8446-0.47580.69630.965-0.08791.1396-0.86650.6931-0.38210.5679-0.17350.31790.2209-0.18220.4411-8.8620.9662-45.998
201.0123-0.1775-0.41022.783-2.05023.60430.46610.11960.48420.2706-0.33760.97120.03490.2698-0.05870.2883-0.03230.14210.2884-0.07860.4252-14.067113.0808-54.4147
210.2848-0.7882-0.41274.53133.39342.753-0.0227-0.14640.0195-0.0731-0.3272-0.1711-0.1014-0.54720.30430.620.23780.21580.5706-0.12790.8144-21.129221.492-54.2581
221.2086-0.2939-0.22992.98880.08511.2271-0.0647-0.3568-0.1206-0.20730.15750.23470.15160.0852-0.02730.2386-0.12720.0670.1753-0.08180.2077-12.49996.4555-52.5141
230.9898-0.17542.36910.0556-0.4425.77810.453-0.1831-0.17290.7699-0.2236-0.02440.23090.591-0.10140.5952-0.14060.11940.3499-0.13180.1592-6.51680.8164-48.4159
241.20561.23292.10651.27822.15683.7349-0.1464-0.52290.3660.515-0.0196-0.32090.19040.9372-0.02730.6834-0.1960.10610.586-0.09010.4019-8.96087.2353-38.8093
250.46070.1615-0.35350.18580.25351.67410.1419-0.3650.6390.17080.39941.1953-0.15170.0023-0.15980.4553-0.04570.28890.3666-0.16520.4-19.048510.5874-42.7471
260.79460.41051.26482.8470.31552.0718-0.48120.36410.2953-0.0965-0.87970.60890.1324-0.07310.68190.2607-0.0558-0.00220.3683-0.14120.7384-19.8790.2459-58.2338
270.96670.5738-0.59021.451-0.38062.18280.0322-0.1499-0.17760.3845-0.53990.87870.3878-0.12040.19690.5195-0.140.18420.3027-0.14440.3499-17.9541-1.0575-46.6013
280.00530.0223-0.02383.0203-0.87740.2457-0.14110.1056-0.36590.6247-0.26290.26870.25410.01890.33991.5166-0.43520.64790.5944-0.13180.6888-19.5283.1953-35.9305
290.57370.66390.31880.80260.29530.13940.6680.15020.3068-0.8095-0.22970.6192-0.23570.2781-0.10950.49470.01510.15790.4008-0.07710.5731-25.26486.7962-54.2749
30-0.030.1339-0.05810.06550.032-0.0483-0.06290.42940.49860.3252-0.30911.17490.6654-0.86980.20440.3731-0.03710.23710.5087-0.11450.9695-25.285213.1857-55.5474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 17:24)A17 - 24
2X-RAY DIFFRACTION2(chain A and resid 25:39)A25 - 39
3X-RAY DIFFRACTION3(chain A and resid 40:58)A40 - 58
4X-RAY DIFFRACTION4(chain A and resid 59:63)A59 - 63
5X-RAY DIFFRACTION5(chain A and resid 64:69)A64 - 69
6X-RAY DIFFRACTION6(chain A and resid 70:81)A70 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:91)A82 - 91
8X-RAY DIFFRACTION8(chain A and resid 92:97)A92 - 97
9X-RAY DIFFRACTION9(chain A and resid 98:118)A98 - 118
10X-RAY DIFFRACTION10(chain A and resid 119:141)A119 - 141
11X-RAY DIFFRACTION11(chain A and resid 142:146)A142 - 146
12X-RAY DIFFRACTION12(chain A and resid 147:167)A147 - 167
13X-RAY DIFFRACTION13(chain A and resid 168:176)A168 - 176
14X-RAY DIFFRACTION14(chain A and resid 177:186)A177 - 186
15X-RAY DIFFRACTION15(chain A and resid 187:196)A187 - 196
16X-RAY DIFFRACTION16(chain D and resid 18:31)D18 - 31
17X-RAY DIFFRACTION17(chain D and resid 32:43)D32 - 43
18X-RAY DIFFRACTION18(chain D and resid 44:58)D44 - 58
19X-RAY DIFFRACTION19(chain D and resid 59:79)D59 - 79
20X-RAY DIFFRACTION20(chain D and resid 80:91)D80 - 91
21X-RAY DIFFRACTION21(chain D and resid 92:97)D92 - 97
22X-RAY DIFFRACTION22(chain D and resid 98:116)D98 - 116
23X-RAY DIFFRACTION23(chain D and resid 117:123)D117 - 123
24X-RAY DIFFRACTION24(chain D and resid 124:131)D124 - 131
25X-RAY DIFFRACTION25(chain D and resid 132:141)D132 - 141
26X-RAY DIFFRACTION26(chain D and resid 142:146)D142 - 146
27X-RAY DIFFRACTION27(chain D and resid 147:158)D147 - 158
28X-RAY DIFFRACTION28(chain D and resid 159:164)D159 - 164
29X-RAY DIFFRACTION29(chain D and resid 165:176)D165 - 176
30X-RAY DIFFRACTION30(chain D and resid 177:196)D177 - 196

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