[English] 日本語
Yorodumi
- PDB-3ve5: Structure of recombination mediator protein RecR16-196 deletion mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


DNA recombination / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / RecR, C-terminal / RecR, helix-hairpin-helix / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger motif / RecR protein signature. / Toprim domain ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #80 / RecR, C-terminal / RecR, helix-hairpin-helix / DNA recombination protein RecR / Recombination protein RecR, conserved site / Recombination protein RecR / RecR, TOPRIM domain / RecR, Cys4-zinc finger motif / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Recombination protein recR / Genetic recombination / 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 / Imidazole


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


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more