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- PDB-1vi0: Crystal structure of a transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 1vi0
TitleCrystal structure of a transcriptional regulator
Componentstranscriptional regulator
KeywordsTRANSCRIPTION / structural genomics
Function / homology
Function and homology information


lipid catabolic process / fatty acid metabolic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / : / 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. / Homeodomain-like ...Transcription regulator YsiA, C-terminal / YsiA-like protein, C-terminal region / : / 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DODECYL-COA / Fatty acid metabolism regulator protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 1.65 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)48,2463
Polymers47,2972
Non-polymers9501
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-44 kcal/mol
Surface area15870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.404, 67.436, 98.854
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


Mass: 23648.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yerO / Production host: Escherichia coli (E. coli) / References: UniProt: P94548
#2: Chemical ChemComp-DCC / DODECYL-COA


Mass: 949.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H58N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 1.65→39.87 Å / Num. all: 44220 / Num. obs: 44220 / % possible obs: 96.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 1.5 / % possible all: 89.7
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 89.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 1.65→39.87 Å / σ(F): 0
RfactorNum. reflection
Rfree0.278 2256
Rwork0.231 -
obs-44220
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 463.945 Å2 / ksol: 0.999 e/Å3
Displacement parametersBiso mean: 29.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.927 Å20 Å20 Å2
2--0.935 Å20 Å2
3----0.008 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.65→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 61 257 3280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d2.46
X-RAY DIFFRACTIONp_planar_tor2.913
X-RAY DIFFRACTIONp_chiral_restr0.153
X-RAY DIFFRACTIONp_plane_restr0.015
X-RAY DIFFRACTIONp_mcbond_it1.988
X-RAY DIFFRACTIONp_mcangle_it3.216
X-RAY DIFFRACTIONp_scbond_it3.715
X-RAY DIFFRACTIONp_scangle_it5.088
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.5

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