[English] 日本語
Yorodumi
- PDB-2y75: The Structure of CymR (YrzC) the Global Cysteine Regulator of B. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y75
TitleThe Structure of CymR (YrzC) the Global Cysteine Regulator of B. subtilis
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN
Function / homology
Function and homology information


protein heterooligomerization / core promoter sequence-specific DNA binding / protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator CymR
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShepard, W. / Soutourina, O. / Courtois, E. / England, P. / Haouz, A. / Martin-Verstraete, I.
CitationJournal: FEBS J. / Year: 2011
Title: Insights Into the Rrf2 Repressor Family - the Structure of Cymr, the Global Cysteine Regulator of Bacillus Subtilis.
Authors: Shepard, W. / Soutourina, O. / Courtois, E. / England, P. / Haouz, A. / Martin-Verstraete, I.
History
DepositionJan 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
C: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
E: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
F: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,56225
Polymers84,9196
Non-polymers1,64319
Water15,673870
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19280 Å2
ΔGint-146.5 kcal/mol
Surface area38590 Å2
MethodPISA
2
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
F: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,43015
Polymers42,4593
Non-polymers97112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-151.6 kcal/mol
Surface area22680 Å2
MethodPISA
3
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
C: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
E: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,13210
Polymers42,4593
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-109.2 kcal/mol
Surface area22360 Å2
MethodPISA
4
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
B: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9189
Polymers28,3062
Non-polymers6127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-103.4 kcal/mol
Surface area12480 Å2
MethodPISA
5
C: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
D: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7267
Polymers28,3062
Non-polymers4205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-93.9 kcal/mol
Surface area12780 Å2
MethodPISA
6
E: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
F: HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9189
Polymers28,3062
Non-polymers6127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-97.8 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.700, 103.700, 106.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.674073, 0.300232, -0.674897), (0.351228, -0.673502, -0.650411), (-0.649818, -0.675467, 0.34854)32.212, -64.955, -16.168
2given(-0.113866, 0.989224, -0.092036), (-0.012232, 0.091236, 0.995754), (0.993421, 0.114509, 0.001711)47.942, 3.284, -46.152
3given(-0.596941, -0.717792, 0.358379), (-0.674871, 0.207707, -0.708101), (0.433832, -0.664554, -0.608406)32.018, -20.662, -65.708
4given(-0.100039, -0.023052, 0.994716), (0.987106, 0.123255, 0.10213), (-0.124958, 0.992107, 0.010424)50.77, -42.198, 1.535
5given(0.446603, -0.616238, -0.648689), (-0.64726, -0.723074, 0.241284), (-0.617738, 0.312112, -0.721793)-15.808, -19.873, -20.626
DetailsTHE BIOLOGICALLY RELEVANT OLIGOMERIZATION STATE OF THE MOLECULE IS A DIMER (BIOMOLECULES 4,5,6), WHICH HAS BEEN CONFIRMED BY ANALYTICAL CENTRIFUGATION.

-
Components

#1: Protein
HTH-TYPE TRANSCRIPTIONAL REGULATOR CYMR / CYMR / YRZC / CYSTEINE METABOLISM REPRESSOR / RRF2 TRANSCRIPTION FACTOR


Mass: 14153.104 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PDIA5770 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLI5 (NOVAGEN) / References: UniProt: O34527
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA LEU BETWEEN POSITIONS 1 & 2 OF O34527 SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 55 %
Description: STRUCTURE WAS SOLVED WITH DATA COLLECTED ON PROXIMA 1 FROM A CRYSTAL, CYMR_13, OF THE SEMET PROTEIN.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: OPTIMIZATION OF INITIAL HITS WAS PURSUED MANUALLY IN LINBRO PLATES WITH A HANGING DROP SETUP. THE BEST CRYSTALS WERE OBTAINED BY MIXING 1.5 UL OF NATIVE CYMR PROTEIN OR SELENOMETHIONINE ...Details: OPTIMIZATION OF INITIAL HITS WAS PURSUED MANUALLY IN LINBRO PLATES WITH A HANGING DROP SETUP. THE BEST CRYSTALS WERE OBTAINED BY MIXING 1.5 UL OF NATIVE CYMR PROTEIN OR SELENOMETHIONINE LABELED PROTEIN AT 14 MG/ML WITH 1.5 UL OF THE RESERVOIR SOLUTION CONTAINING 1.6 M AMMONIUM SULPHATE AND 0.1 M TRIS-HCL PH 8.5 AT 18 C DEGREES. THE CRYSTALS APPEARED WITHIN ONE WEEK AND HAD DIMENSIONS OF UP TO 0.1 MM X 0.1 MM X 0.2 MM. A SINGLE CRYSTAL OF THE CYMR PROTEIN WAS FLASH-FROZEN IN LIQUID NITROGEN USING A MIXTURE OF 50% PARATONE AND 50% PARAFFIN OIL AS CRYOPROTECTANT.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.983
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2→17.84 Å / Num. obs: 73831 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.64 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.42
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.03 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→17.84 Å / Cor.coef. Fo:Fc: 0.9537 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0
Details: MISSING RESIDUES - 60A-63A 130C -139C, 129D-139D, 130E-139E, 130F-139F. MISSING SIDECHAINS - 92C. RESIDUES WITH MULTIPLE CONFORMATIONS - 123A, 20B, 44B, 44D, 57D, 81E, 6F, 98F. UNIDENTIFIED ...Details: MISSING RESIDUES - 60A-63A 130C -139C, 129D-139D, 130E-139E, 130F-139F. MISSING SIDECHAINS - 92C. RESIDUES WITH MULTIPLE CONFORMATIONS - 123A, 20B, 44B, 44D, 57D, 81E, 6F, 98F. UNIDENTIFIED FOFC OBJECTS, UFOS. UFO-1, FLATTENED BLOB NEAR N THR-6, POSSIBLE MIXTURE OF SULPHATE AND CHLORIDE ANIONS, LOCATED INSIDE HEXAMER. UFO-2, ELONGATED AND BRANCHED BLOB NEAR OG SER-28, POSSIBLE DISORDER IN CRYSTAL CONTACTS WITH C- -TERMINI. UFO-3, ELONGATED AND BRANCHED BLOB NEAR N GLY-25, POSSIBLE DISORDER IN CRYSTAL CONTACTS WITH C- TERMINI. UFO-4, EXTENDED AND BRANCHED BLOB NEAR N GLU-40 AND SER- -39, POSSIBLE DISORDER IN CRYSTAL CONTACT WITH ARG-82 SIDECHAIN. UNIDENTIFIED FOFC DENSITY OBJECTS OCCUR NEAR N THR-6, OG SER-28, N GLY-25, N GLU-40 AND SER-39. ATTEMPTS TO MODEL THESE BLOBS CORRECTLY AS WATERS, CHLORIDES OR SULPHATES WERE UNSUCCESSFUL. THESE BLOBS OR UFOS HAVE BEEN LEFT UNMODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 3715 5.04 %RANDOM
Rwork0.1871 ---
obs0.1884 73692 --
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.5589 Å20 Å20 Å2
2--0.1613 Å20 Å2
3----0.7201 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2→17.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 83 870 6831
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016081HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.098250HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2184SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes862HARMONIC5
X-RAY DIFFRACTIONt_it6081HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion823SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7705SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 281 5.16 %
Rwork0.2201 5169 -
all0.2202 5450 -

+
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