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- PDB-6eni: Tryptophan Repressor TrpR from E.coli variant T44L S88Y with Indo... -

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Basic information

Entry
Database: PDB / ID: 6eni
TitleTryptophan Repressor TrpR from E.coli variant T44L 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 / Resolution: 1.1 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 4, 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)27,4715
Polymers27,0592
Non-polymers4123
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-24 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.780, 63.410, 64.770
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: 13529.434 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


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MMT buffer pH 4 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2013
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.1→34.915 Å / Num. obs: 87129 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 12.692 % / Biso Wilson estimate: 10.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.053 / Χ2: 0.982 / Net I/σ(I): 26.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.1310.7220.7243.9851920.9010.7677
1.13-1.1613.2230.4756.260160.9660.49491.4
1.16-1.1913.2850.3637.7759670.9790.37792.8
1.19-1.2312.090.3848.0857200.9730.40192.4
1.23-1.2713.1870.24110.9957360.9890.2594.5
1.27-1.3112.7640.25312.154420.9880.26393.7
1.31-1.3613.2980.14816.4253730.9950.15495.4
1.36-1.4212.4420.12118.3152180.9960.12795.9
1.42-1.4813.2160.11222.9850370.9970.11696.1
1.48-1.5513.6570.07230.6848230.9980.07496.9
1.55-1.6413.4530.06135.3246200.9990.06397.2
1.64-1.7412.4510.05337.9244290.9990.05697.7
1.74-1.8613.5280.04845.2141640.9990.0597.9
1.86-2.0112.3150.04748.0238910.9990.0598.2
2.01-2.212.9090.04155.6536120.9990.04398.4
2.2-2.4610.660.03953.6133030.9990.04199.2
2.46-2.8412.8230.03561.6229310.9990.03799.3
2.84-3.4812.5640.03563.6225170.9990.03699.6
3.48-4.9210.8630.04160.3619840.9990.04399.6
4.92-34.91512.2230.04164.1911540.9980.04399.4

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Processing

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

1tro


Resolution: 1.1→34.915 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1755 4356 5 %
Rwork0.1582 --
obs0.1591 87117 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.19 Å2 / Biso mean: 16.8527 Å2 / Biso min: 4.88 Å2
Refinement stepCycle: final / Resolution: 1.1→34.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 52 467 2212
Biso mean--14.57 25.44 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011875
X-RAY DIFFRACTIONf_angle_d1.082550
X-RAY DIFFRACTIONf_chiral_restr0.075277
X-RAY DIFFRACTIONf_plane_restr0.008340
X-RAY DIFFRACTIONf_dihedral_angle_d20.682733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0993-1.11180.20881040.22531969207368
1.1118-1.12490.32681250.30562383250883
1.1249-1.13860.24781380.24992618275690
1.1386-1.1530.18751390.18892647278692
1.153-1.16820.20091410.19222666280792
1.1682-1.18420.20151400.19142661280193
1.1842-1.20110.21691440.19612736288094
1.2011-1.21910.25531390.23682653279292
1.2191-1.23810.26671410.24092678281993
1.2381-1.25840.19421440.18552733287795
1.2584-1.28010.17731450.17662744288995
1.2801-1.30340.26431420.23842690283292
1.3034-1.32850.20811450.17932762290795
1.3285-1.35560.18221450.16882765291096
1.3556-1.38510.20891450.16942754289996
1.3851-1.41730.181480.16922807295596
1.4173-1.45270.19551470.16732792293996
1.4527-1.4920.16251480.16312806295496
1.492-1.53590.16391490.14862838298797
1.5359-1.58550.15831480.14672813296197
1.5855-1.64220.15571490.14622827297697
1.6422-1.70790.16141510.14422866301797
1.7079-1.78560.16881500.14822844299498
1.7856-1.87980.15511510.14942871302298
1.8798-1.99750.1591530.14532904305798
1.9975-2.15170.15261530.13612917307099
2.1517-2.36820.15591540.1342916307099
2.3682-2.71080.171560.14332969312599
2.7108-3.41490.16681580.141430063164100
3.4149-34.93240.17991640.164231263290100

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