[English] 日本語
Yorodumi
- PDB-6qua: The complex structure of hsRosR-SG (vng0258/RosR-SG) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qua
TitleThe complex structure of hsRosR-SG (vng0258/RosR-SG)
Components
  • (DNA (28-MER)) x 2
  • hsRosR-DNA binding protein
KeywordsDNA BINDING PROTEIN / Halophiles / wHTH DNA binding protein / RosR / High salt medium / Protein-DNA interactions
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / : / DNA / DNA (> 10) / PadR family transcription regulator RosR
Function and homology information
Biological speciesHalobacterium salinarum (Halophile)
Halobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.681 Å
AuthorsShaanan, B. / Kutnowski, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1382/13 Israel
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.
Authors: Kutnowski, N. / Shmulevich, F. / Davidov, G. / Shahar, A. / Bar-Zvi, D. / Eichler, J. / Zarivach, R. / Shaanan, B.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.ref_id
Revision 2.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hsRosR-DNA binding protein
B: hsRosR-DNA binding protein
C: hsRosR-DNA binding protein
D: hsRosR-DNA binding protein
E: DNA (28-MER)
F: DNA (28-MER)
G: DNA (28-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,16525
Polymers87,6978
Non-polymers1,46917
Water91951
1
A: hsRosR-DNA binding protein
B: hsRosR-DNA binding protein
E: DNA (28-MER)
F: DNA (28-MER)
hetero molecules


  • defined by author
  • Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., ...Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., isothermal titration calorimetry, The binding stoichiometry was approximately one, indicating that one protein dimer bound a single sequence.
  • 44.7 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)44,68614
Polymers43,8484
Non-polymers83710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hsRosR-DNA binding protein
D: hsRosR-DNA binding protein
G: DNA (28-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,48011
Polymers43,8484
Non-polymers6317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.279, 84.665, 90.400
Angle α, β, γ (deg.)81.91, 87.13, 75.61
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
hsRosR-DNA binding protein


Mass: 13317.591 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile)
Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: VNG_0258H / Production host: Haloferax volcanii (archaea) / Strain (production host): WR341 / References: UniProt: Q9HSF4

-
DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (28-MER)


Mass: 8655.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile) / References: UniProt: Q9HSF4*PLUS
#3: DNA chain DNA (28-MER)


Mass: 8557.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile)

-
Non-polymers , 3 types, 68 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide, DNA/hsRosR ratio = 1.83. 2.96 M (NH4)2SO4, 30 mM MnCl2 and 0.02% azide.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.56→45.79 Å / Num. obs: 22780 / % possible obs: 84.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.4
Reflection shellResolution: 2.56→2.839 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4) but with the SG sequence.

6fdh

4fx4


Resolution: 2.681→45.79 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.8
RfactorNum. reflection% reflection
Rfree0.2893 1082 5.14 %
Rwork0.2381 --
obs0.2407 21032 55.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.681→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 2296 69 52 6061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046324
X-RAY DIFFRACTIONf_angle_d0.6349043
X-RAY DIFFRACTIONf_dihedral_angle_d23.363568
X-RAY DIFFRACTIONf_chiral_restr0.0341007
X-RAY DIFFRACTIONf_plane_restr0.003782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6807-2.80270.4387350.388602X-RAY DIFFRACTION13
2.8027-2.95040.3662560.36621217X-RAY DIFFRACTION27
2.9504-3.13520.4073980.35051647X-RAY DIFFRACTION37
3.1352-3.37720.34541160.31552085X-RAY DIFFRACTION47
3.3772-3.71690.33451390.30432492X-RAY DIFFRACTION56
3.7169-4.25450.32151780.25053423X-RAY DIFFRACTION76
4.2545-5.35880.29352340.21844247X-RAY DIFFRACTION95
5.3588-45.79720.21922260.18384237X-RAY DIFFRACTION95
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)
16.3247-2.6356-3.79456.8121-0.28643.91370.19562.1319-0.0271-2.1746-0.1854-0.57780.11210.1218-0.19921.32660.1772-0.06741.1073-0.20510.612215.1824-15.5854-22.4579
28.0043-2.70460.72115.79710.91972.45750.02620.4843-0.0805-0.3940.3232-0.65430.26090.4744-0.22910.39460.0250.02690.2995-0.04370.239311.2643-18.7108-10.7109
34.47210.5113-3.07241.8471-1.87033.4-0.1736-0.31540.89030.25390.5670.3962-0.14540.1517-0.36440.9990.1391-0.15510.2853-0.0880.727310.3324-27.374-3.4127
44.4148-0.0929-0.02956.929-0.07184.4243-0.4038-0.7692-0.4542-0.04060.52371.04460.1928-0.6578-0.10860.30150.0588-0.02890.48730.25850.6561.456-19.0004-4.9849
52.1464-0.7845-0.22730.91781.29642.3428-0.21440.4451-0.943-0.58230.3957-0.14050.66410.1888-0.25030.8899-0.1625-0.04890.2925-0.19520.72558.2026-27.711-15.7518
66.8052-1.7983-1.70831.1019-0.13280.9735-0.23740.4307-0.4793-1.11730.18410.35170.8544-0.23930.06081.5985-0.0343-0.3820.43460.07231.33095.6044-39.4743-5.0111
75.3472-2.069-0.11153.57731.29934.7624-0.3886-0.0129-0.9006-0.19430.0888-0.26251.16880.16590.34010.95650.23080.19350.2992-0.10370.68113.4099-29.9424-10.0618
81.99981.1904-0.23682.4145-1.77652.8651-0.18250.7344-0-0.6841-0.0301-0.79540.50660.77730.08610.2960.15510.06730.51710.02690.70122.1506-10.3809-13.6043
96.2606-0.0210.46355.2227-2.02653.523-0.0468-0.3211-0.20080.15170.1473-0.1782-0.01350.35840.1344-0.0588-0.0054-0.10920.56790.05230.506622.6337-5.06171.3602
104.542-2.49763.85664.785-4.88536.13360.1737-1.3584-0.72521.12830.14471.4653-0.0696-1.2172-0.39380.5242-0.15060.11270.63880.13180.59063.4197-4.0965-7.9648
114.7669-0.2263-0.57984.331-0.48279.1814-0.2976-0.4099-0.26770.00920.0147-0.29560.00580.73930.2090.2110.1052-0.04110.45550.09760.158612.5983-1.9461-17.6695
126.412-1.67631.08591.7740.4939.2887-0.30321.13140.7661-1.2635-0.1363-0.96160.17561.59680.38590.76010.02720.05820.64250.23720.423817.150.9503-25.1311
134.758-0.5486-0.45021.2609-3.30089.43520.06970.51790.1656-0.53390.22760.2998-0.4461-0.2018-0.06850.7394-0.0977-0.27850.42130.09330.34716.62913.4537-23.9068
141.4756-0.7330.57032.78860.20491.97010.21650.1631-0.0553-0.3730.0232-0.1602-0.24910.35260.1592-0.13790.1442-0.03040.46730.3390.733619.4349-3.8173-9.1644
151.72070.26690.04735.86014.7823.91930.00190.8242-0.3064-0.77710.1662-0.17930.68811.0022-0.12591.06660.3643-0.03150.942-0.0040.29959.3387-11.016216.6123
166.68140.49340.27123.39082.36442.68930.0795-0.27230.86480.7819-0.29420.8846-1.4428-0.47210.15450.69160.05390.07560.2682-0.02430.36282.60865.678514.6277
176.1161-0.0546-0.08592.44152.20892.81420.09590.15320.90690.13020.2497-0.5376-1.03180.526-0.21050.5049-0.13920.01930.4169-0.01910.267714.01995.197710.5107
181.53090.36060.01060.94030.23970.5803-0.02450.0378-0.4734-0.00830.1384-0.40360.20410.4721-0.0580.06460.15310.06150.44120.1340.56720.9635-12.27229.1592
196.8861-2.91370.99643.2546-1.19984.61190.2235-0.018-0.27770.1611-0.04880.0737-0.2384-0.24190.02870.10180.1521-0.02380.43640.30650.6145-15.1454-7.86476.3372
203.28552.6041-0.96237.3351-4.23225.8944-0.2681-0.3285-0.52430.39480.24071.072-0.0653-0.3063-0.34190.43220.10590.21550.6810.38710.5228-2.1558-15.605423.5111
211.23220.15070.14442.5005-0.14193.17850.3484-0.6234-0.43580.7326-0.12530.49670.3741-0.324-0.12660.18910.08840.1370.54790.45590.6888-6.2183-14.277219.9191
222.17610.01040.05532.10660.34371.6666-0.00850.74810.4451-0.7176-0.11460.1801-0.477-0.0568-0.02062.1016-0.03010.0021.4870.79220.996912.837215.1744-45.3393
230.0654-0.19360.35526.56071.63653.1539-0.65341.13570.3805-2.11230.25911.26110.8287-0.5089-0.04121.1021-0.1901-0.29410.80090.27580.63912.95076.2315-32.829
241.95372.48860.78173.17321.00030.344-0.60641.24550.5315-1.19820.25370.636-0.83710.21350.47242.0905-0.1576-0.37021.6261-0.01080.6017-3.7499-11.5343-34.2931
257.03353.382.75622.19280.2124.3626-0.49291.1105-0.3101-1.47410.91921.64051.5854-0.9333-0.23581.0282-0.1929-0.20640.7150.10130.9249-6.6797-21.2419-18.09
264.92492.08250.77513.6756-1.11442.51690.3061-0.1137-0.95820.1180.35831.5359-0.4172-0.0922-0.51452.004-0.2901-0.08290.5930.14031.6385-5.6579-40.2046-5.9909
274.20380.59180.41067.66821.39590.37760.25490.3458-0.3021-0.65430.3042.1041.09-1.0993-0.30490.9529-0.3386-0.31080.71390.06651.3153-7.2458-30.8648-12.6271
282.279-0.62870.35771.3594-0.27710.0837-0.01511.17540.6719-0.8679-0.174-0.1041-0.33140.02860.1011.7495-0.0619-0.11870.83370.21330.42415.46886.3145-37.45
297.79971.3485-1.993.26391.92082.20310.0521-0.88850.76561.4777-0.01260.5015-0.69770.8963-0.15591.4958-0.193-0.21110.5948-0.05730.700615.7315.292622.3944
301.05681.061-1.08681.4505-1.19231.14620.3095-0.6509-0.40360.8607-0.392-0.1390.71010.2280.20411.6696-0.1081-0.00061.3450.85511.19585.9098-25.970939.5409
311.4071-0.1577-0.52771.81680.7793.0870.0468-0.4011-0.37570.718-0.1631-0.04990.99510.30480.42751.4625-0.1465-0.02461.18851.00811.13963.9753-30.785440.3904
323.79340.4173-0.87360.09280.09960.88740.2389-0.6030.8411.0174-0.15480.1109-0.92531.0241-0.05981.7084-0.2892-0.18120.6712-0.07460.514115.93939.988224.1861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 33 )
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 49 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 70 )
6X-RAY DIFFRACTION6chain 'A' and (resid 71 through 75 )
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 81 )
8X-RAY DIFFRACTION8chain 'A' and (resid 82 through 102 )
9X-RAY DIFFRACTION9chain 'A' and (resid 103 through 121 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 28 )
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 44 )
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 72 )
14X-RAY DIFFRACTION14chain 'B' and (resid 73 through 121 )
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 16 )
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 49 )
17X-RAY DIFFRACTION17chain 'C' and (resid 50 through 81 )
18X-RAY DIFFRACTION18chain 'C' and (resid 82 through 99 )
19X-RAY DIFFRACTION19chain 'C' and (resid 100 through 122 )
20X-RAY DIFFRACTION20chain 'D' and (resid 9 through 44 )
21X-RAY DIFFRACTION21chain 'D' and (resid 45 through 122 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 5 )
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 10 )
24X-RAY DIFFRACTION24chain 'E' and (resid 11 through 15 )
25X-RAY DIFFRACTION25chain 'E' and (resid 16 through 20 )
26X-RAY DIFFRACTION26chain 'E' and (resid 21 through 28 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 15 )
28X-RAY DIFFRACTION28chain 'F' and (resid 16 through 28 )
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 15 )
30X-RAY DIFFRACTION30chain 'G' and (resid 16 through 28 )
31X-RAY DIFFRACTION31chain 'H' and (resid 1 through 10 )
32X-RAY DIFFRACTION32chain 'H' and (resid 11 through 28 )

+
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://pdbjlvh1.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