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- PDB-2y75: The Structure of CymR (YrzC) the Global Cysteine Regulator of B. ... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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.

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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

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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: 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.

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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

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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 -

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