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- PDB-6elg: Tryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y... -

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Basic information

Entry
Database: PDB / ID: 6elg
TitleTryptophan Repressor TrpR from E.coli variant M42F T44L T81I S88Y with Indole-3-acetonitrile
ComponentsTrp operon repressor
KeywordsTRANSCRIPTION / Ligand Binding
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1H-indol-3-ylacetonitrile / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsStiel, A.C. / Shanmugaratnam, S. / Herud-Sikimic, O. / Juergens, G. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHO 4022/2-3 Germany
CitationJournal: Nature / Year: 2021
Title: A biosensor for the direct visualization of auxin
Authors: Herud-Sikimic, O. / Stiel, A.C. / Kolb, M. / Shanmugaratnam, S. / Berendzen, K.W. / Feldhaus, C. / Hocker, B. / Juergens, G.
History
DepositionSep 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trp operon repressor
B: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4274
Polymers27,1152
Non-polymers3122
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-38 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.014, 63.468, 65.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trp operon repressor


Mass: 13557.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A881
#2: Chemical ChemComp-3BO / 1H-indol-3-ylacetonitrile


Mass: 156.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammonium Formate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.38→42.09 Å / Num. obs: 47916 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.28 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.067 / Χ2: 0.971 / Net I/σ(I): 16.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.38-1.415.6360.8021.7933080.6990.88195
1.41-1.456.0310.7032.2934340.7780.7799.9
1.45-1.496.030.5263.1933210.8670.57799.9
1.49-1.545.6690.4343.8632190.9060.47999.7
1.54-1.596.280.3324.7531570.9480.363100
1.59-1.646.5110.2735.9230340.9590.297100
1.64-1.716.5750.2316.9829380.9720.251100
1.71-1.786.5060.1938.3928400.9790.2199.9
1.78-1.866.4390.15510.3827180.9850.168100
1.86-1.955.8060.12612.626020.990.13999.9
1.95-2.056.8470.09217.824930.9950.1100
2.05-2.186.7120.07222.523450.9970.079100
2.18-2.336.650.05927.1322280.9970.064100
2.33-2.516.5770.05130.8620840.9980.055100
2.51-2.755.8610.04333.6319090.9990.04899.8
2.75-3.086.7970.03642.8317360.9990.039100
3.08-3.556.7060.02953.9715580.9990.03199.9
3.55-4.356.3540.02459.1913190.9990.02799.8
4.35-6.155.8720.02257.72105410.024100
6.15-42.096.4050.01964.616190.9990.02199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.29 Å42.09 Å
Translation6.29 Å42.09 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tro

1tro


Resolution: 1.38→42.09 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.02
RfactorNum. reflection% reflection
Rfree0.1765 2396 5 %
Rwork0.1432 --
obs0.1449 47907 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.08 Å2 / Biso mean: 19.8368 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 1.38→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 40 378 2123
Biso mean--13.49 29.75 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011854
X-RAY DIFFRACTIONf_angle_d0.9942520
X-RAY DIFFRACTIONf_chiral_restr0.066277
X-RAY DIFFRACTIONf_plane_restr0.007331
X-RAY DIFFRACTIONf_dihedral_angle_d21.843720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3761-1.40420.3291290.26372458258794
1.4042-1.43480.25091390.20826312770100
1.4348-1.46810.27661400.204326672807100
1.4681-1.50490.21071400.165126462786100
1.5049-1.54550.18351390.160826492788100
1.5455-1.5910.19141390.139326502789100
1.591-1.64240.18061410.133126792820100
1.6424-1.70110.17121400.12926522792100
1.7011-1.76920.16071420.131426962838100
1.7692-1.84970.17541390.132926492788100
1.8497-1.94720.15561410.133326802821100
1.9472-2.06920.15661430.127526992842100
2.0692-2.2290.20751410.12326852826100
2.229-2.45330.14821430.123327112854100
2.4533-2.80820.16491420.132627172859100
2.8082-3.53780.1711460.14127682914100
3.5378-42.10960.16851520.157328743026100

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