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- PDB-2yve: Crystal structure of the methylene blue-bound form of the multi-d... -

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Basic information

Entry
Database: PDB / ID: 2yve
TitleCrystal structure of the methylene blue-bound form of the multi-drug binding transcriptional repressor CgmR
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / transcriptional regulator / helix-turn-helix / TetR-family
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
TetR transcriptional regulator CgmR-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / Transcriptional regulator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsItou, H. / Shirakihara, Y. / Tanaka, I.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of the Multidrug Binding Repressor Corynebacteriumglutamicum CgmR in Complex with Inducers and with an Operator
Authors: Itou, H. / Watanabe, N. / Yao, M. / Shirakihara, Y. / Tanaka, I.
History
DepositionApr 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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 / 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 / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,86911
Polymers42,7122
Non-polymers1,1579
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-42 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 67.360, 101.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator / Bacterial regulatory protein / TetR family / CGL2612


Mass: 21356.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC13032 / Gene: cgl2612 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NMG3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MBT / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / METHYLENE BLUE


Mass: 284.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N3S / Comment: medication*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Cacodylate, 0.1M MgCl2, 8% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 78066 / Num. obs: 78066 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.228 / Num. unique all: 7625 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V7B

1v7b
PDB Unreleased entry


Resolution: 1.4→9.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1296929.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 7713 9.9 %RANDOM
Rwork0.203 ---
all-81799 --
obs-77945 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.5288 Å2 / ksol: 0.585223 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.64 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.4→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 77 322 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.452
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 1224 9.8 %
Rwork0.209 11258 -
obs-11258 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PARAM:MTB_GOL_CAC.paramPARAM:MTB_GOL_CAC.top

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