[English] 日本語
Yorodumi
- PDB-6hse: Structure of dithionite-reduced RsrR in spacegroup P2(1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hse
TitleStructure of dithionite-reduced RsrR in spacegroup P2(1)
ComponentsRrf2 family transcriptional regulator
KeywordsTRANSCRIPTION / REDOX SENSOR / IRON SULFUR CLUSTER
Function / homology
Function and homology information


Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / SULFITE ION / Rrf2 family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues.
Authors: Volbeda, A. / Martinez, M.T.P. / Crack, J.C. / Amara, P. / Gigarel, O. / Munnoch, J.T. / Hutchings, M.I. / Darnault, C. / Le Brun, N.E. / Fontecilla-Camps, J.C.
History
DepositionOct 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
B: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,61112
Polymers69,5444
Non-polymers1,0688
Water1,33374
1
A: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3006
Polymers34,7722
Non-polymers5284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-87 kcal/mol
Surface area14640 Å2
MethodPISA
2
B: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3126
Polymers34,7722
Non-polymers5404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-86 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.270, 94.110, 97.800
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ACBD

#1: Protein
Rrf2 family transcriptional regulator


Mass: 17385.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_6563 / Plasmid: pGS-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2RGC9

-
Non-polymers , 5 types, 82 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: NaCl, PEG6000, MES, dithionite, anaerobic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→47.05 Å / Num. obs: 29137 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.076 / Rrim(I) all: 0.179 / Net I/σ(I): 8.9 / Num. measured all: 155123
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.385.52.17728380.3011.0222.4199.6
8.91-47.0550.0355170.9980.0170.03999.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200012168

Resolution: 2.3→47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.851 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.255 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1378 4.8 %RANDOM
Rwork0.2285 ---
obs0.23 27474 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.24 Å2 / Biso mean: 62.603 Å2 / Biso min: 33.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-1.41 Å2
2--0.27 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4611 0 36 74 4721
Biso mean--45.56 41.24 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194766
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9916521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45123.092152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04315723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8011536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223534
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 100 -
Rwork0.378 1812 -
all-1912 -
obs--89.64 %
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)
11.1376-0.1920.60521.4196-0.73832.0643-0.1531-0.07530.12190.09610.12560.04740.0609-0.21820.02750.1140.0099-0.06820.0321-0.03860.20988.173119.9426-0.935
20.3844-0.07890.49060.8933-0.94872.53580.06570.06490.00470.2113-0.0215-0.24080.17530.3756-0.04420.27020.0821-0.18250.0881-0.05620.217925.020311.481417.9663
31.313-1.02181.99441.1733-1.81653.78590.0347-0.3582-0.2292-0.00040.33030.33640.1266-0.742-0.36510.11540.0169-0.05630.22820.0670.25883.725338.728329.7424
40.9738-0.72691.56621.585-1.72883.8383-0.0389-0.16170.1541-0.02560.0936-0.22830.1034-0.2462-0.05480.05050.0076-0.06710.0376-0.01810.179925.029132.03644.1402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 161
2X-RAY DIFFRACTION1A170
3X-RAY DIFFRACTION2C1 - 159
4X-RAY DIFFRACTION2C170
5X-RAY DIFFRACTION3B1 - 158
6X-RAY DIFFRACTION3B170
7X-RAY DIFFRACTION4D1 - 160
8X-RAY DIFFRACTION4D170

+
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