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- PDB-6enn: Tryptophan Repressor TrpR from E.coli variant T44L T81M N87G S88Y... -

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Basic information

Entry
Database: PDB / ID: 6enn
TitleTryptophan Repressor TrpR from E.coli variant T44L T81M N87G S88Y with Indole-3-acetic acid as ligand
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-YLACETIC ACID / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 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
DepositionOct 5, 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)27,3554
Polymers27,0052
Non-polymers3502
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-32 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.577, 63.185, 64.904
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: 13502.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A881
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID / Indole-3-acetic acid


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MMT buffer pH 5 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2014
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→41.772 Å / Num. obs: 75208 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.836 % / Biso Wilson estimate: 12.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 0.991 / Net I/σ(I): 16.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.17-1.23.8060.6352.0546630.6990.73383.7
1.2-1.235.1560.6243.0252230.8530.69695.9
1.23-1.275.5730.4773.6652840.8760.52799.8
1.27-1.315.3490.4764.3648490.9060.52994.7
1.31-1.355.530.3065.549930.9460.33899.9
1.35-1.45.9960.2486.9548140.9660.272100
1.4-1.456.0660.2118.1546610.9770.231100
1.45-1.515.9930.1511.4544890.9880.16599.6
1.51-1.585.9990.10914.1743050.9920.11999.9
1.58-1.666.5440.09117.641290.9950.099100
1.66-1.746.5630.07620.6639250.9960.082100
1.74-1.856.440.06324.3137440.9970.068100
1.85-1.985.7420.05926.8234590.9950.06598.7
1.98-2.146.7290.04733.4932750.9980.051100
2.14-2.346.1930.04634.8630230.9970.05199.5
2.34-2.626.2160.04136.6927640.9980.04599.9
2.62-3.026.1360.03838.4824480.9980.04299.8
3.02-3.76.4330.03841.320670.9980.04199.6
3.7-5.235.8240.03640.116450.9980.0499.5
5.23-41.7726.1450.03741.149600.9980.04199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.29 Å41.77 Å
Translation6.29 Å41.77 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
Resolution: 1.17→41.772 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.59
RfactorNum. reflection% reflection
Rfree0.18 3738 5 %
Rwork0.1483 --
obs0.1499 74759 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.6 Å2 / Biso mean: 18.6712 Å2 / Biso min: 8.04 Å2
Refinement stepCycle: final / Resolution: 1.17→41.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 42 345 2084
Biso mean--13.63 31.09 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011912
X-RAY DIFFRACTIONf_angle_d1.1032609
X-RAY DIFFRACTIONf_chiral_restr0.076280
X-RAY DIFFRACTIONf_plane_restr0.008350
X-RAY DIFFRACTIONf_dihedral_angle_d21.082773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1704-1.18520.25261030.23311939204273
1.1852-1.20080.27941310.22482491262294
1.2008-1.21720.38791330.32772511264495
1.2172-1.23460.44561350.42052579271497
1.2346-1.2530.19111390.1826322771100
1.253-1.27260.19521400.176826592799100
1.2726-1.29350.27791340.2792539267396
1.2935-1.31580.39321330.30992539267295
1.3158-1.33970.15281410.134226672808100
1.3397-1.36550.15511400.118426732813100
1.3655-1.39340.15481410.111426662807100
1.3934-1.42370.14751370.112926162753100
1.4237-1.45680.18061410.116126722813100
1.4568-1.49320.17611400.122226652805100
1.4932-1.53360.1261400.100326622802100
1.5336-1.57870.14651420.099426852827100
1.5787-1.62970.13121400.095326752815100
1.6297-1.68790.15021400.104126462786100
1.6879-1.75550.13761420.108127032845100
1.7555-1.83540.13411410.114326742815100
1.8354-1.93220.18831380.17312667280599
1.9322-2.05320.16941410.123826832824100
2.0532-2.21170.14851430.121227142857100
2.2117-2.43430.17471420.14992689283199
2.4343-2.78650.16741440.138927372881100
2.7865-3.51040.18181450.146227652910100
3.5104-41.79820.1931520.16742873302599

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