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- PDB-1irq: Crystal structure of omega transcriptional repressor at 1.5A reso... -

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Basic information

Entry
Database: PDB / ID: 1irq
TitleCrystal structure of omega transcriptional repressor at 1.5A resolution
Componentsomega transcriptional repressor
KeywordsGENE REGULATION / transcriptional repressor / ribbon-helix-helix
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Omega transcriptional repressor / Omega Transcriptional Repressor / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsMurayama, K. / Orth, P. / De La Hoz, A.B. / Alonso, J.C. / Saenger, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution.
Authors: Murayama, K. / Orth, P. / de la Hoz, A.B. / Alonso, J.C. / Saenger, W.
History
DepositionOct 11, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: omega transcriptional repressor
B: omega transcriptional repressor


Theoretical massNumber of molelcules
Total (without water)16,0092
Polymers16,0092
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-28 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.100, 46.100, 88.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein omega transcriptional repressor / hypothetical protein omega


Mass: 8004.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pSM19035 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57468
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.69 Å3/Da / Density % sol: 27.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, 100mM Sodium Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
350 mM1dropNaCl
45 %(v/v)glycerol1drop
530 %(w/v)PEG33501reservoir
6100 mMsodium acetate1reservoir
7100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9073 Å / Relative weight: 1
ReflectionResolution: 1.5→29.6 Å / Num. all: 16703 / Num. obs: 16703 / % possible obs: 97.6 % / Biso Wilson estimate: 24.3 Å2
Reflection
*PLUS
Num. measured all: 69483 / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.52 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.384

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→29.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 652365.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.17
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1623 10 %RANDOM
Rwork0.211 ---
obs0.211 16203 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.6132 Å2 / ksol: 0.317343 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å23.19 Å20 Å2
2--2.67 Å20 Å2
3----5.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 0 125 968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.054
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.68
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 3.17 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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