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- PDB-6ekp: Tryptophan Repressor TrpR from E.coli variant T44L T81M S88Y with... -

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Basic information

Entry
Database: PDB / ID: 6ekp
TitleTryptophan Repressor TrpR from E.coli variant T44L T81M 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 / 3,6,9,12,15-PENTAOXAHEPTADECANE / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 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 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 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)27,7205
Polymers27,1192
Non-polymers6013
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-28 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.035, 63.123, 64.640
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: 13559.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / 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-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 Calcium Chloride 0.1M Bis-Tris pH 6.5 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2014
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.46→41.904 Å / Num. obs: 39396 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.292 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.038 / Χ2: 0.985 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.46-1.54.1290.8231.927440.8010.93993.6
1.5-1.544.2260.5962.6827690.8840.67897.6
1.54-1.584.0330.4693.3326990.90.53797.3
1.58-1.634.380.3454.5526260.940.39198.4
1.63-1.684.4760.2476.1625480.970.27998.5
1.68-1.744.4330.1957.7425120.9790.2298.9
1.74-1.814.3370.13410.3824300.9880.15299.4
1.81-1.884.0530.10212.8523180.9930.11799.3
1.88-1.974.4510.07517.3122580.9970.08599.2
1.97-2.064.5380.0562321440.9980.06499.6
2.06-2.174.4640.04228.5220550.9980.04799.6
2.17-2.314.3070.03533.6319650.9980.03999.6
2.31-2.464.1180.03136.8218210.9990.03599.6
2.46-2.664.5520.02842.2717200.9990.03299.8
2.66-2.924.4360.02744.4315920.9990.03199.9
2.92-3.264.2170.02647.0514500.9990.0399.9
3.26-3.764.0250.02648.8612800.9980.02999.3
3.76-4.614.3480.02652.3211080.9980.0399.6
4.61-6.523.9460.02549.928640.9990.02899.3
6.52-41.9043.8190.03249.644930.9970.03895.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.46 Å41.9 Å
Translation1.46 Å41.9 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: 1.46→41.904 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.1897 1970 5 %
Rwork0.1721 --
obs0.173 39386 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.97 Å2 / Biso mean: 39.1988 Å2 / Biso min: 18.41 Å2
Refinement stepCycle: final / Resolution: 1.46→41.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 57 250 1983
Biso mean--29.97 45.44 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021759
X-RAY DIFFRACTIONf_angle_d0.4972370
X-RAY DIFFRACTIONf_chiral_restr0.041258
X-RAY DIFFRACTIONf_plane_restr0.004306
X-RAY DIFFRACTIONf_dihedral_angle_d17.447687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4577-1.49420.32921300.32162473260393
1.4942-1.53460.29651380.26482614275298
1.5346-1.57980.27561370.25432613275097
1.5798-1.63070.26921380.22642618275698
1.6307-1.6890.25861380.2142631276999
1.689-1.75670.21311410.20232673281499
1.7567-1.83660.20331400.18692655279599
1.8366-1.93340.21731410.192926792820100
1.9334-2.05460.21841420.1762700284299
2.0546-2.21320.1691420.163526932835100
2.2132-2.43590.16561420.154127022844100
2.4359-2.78830.18781440.162827402884100
2.7883-3.51270.16881460.162227672913100
3.5127-41.92150.18111510.16252858300999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.82731.53016.41151.77911.43255.81660.0284-0.57470.0375-0.02-0.11020.31130.0488-0.32930.07130.2434-0.00660.02630.25690.00910.25031.6503-19.7858-8.2203
21.4349-1.1342-0.00047.4564-1.17431.1597-0.0377-0.13730.16050.0214-0.0269-0.5378-0.00470.0930.04780.1565-0.00120.00890.26670.0230.22219.046-10.2491-8.4204
37.6752-1.5641-3.54782.11250.93335.1549-0.1230.0880.6527-0.50320.1574-1.1008-0.21030.47890.02290.3859-0.0330.0830.41860.0660.549521.54987.5532-16.0981
48.60093.2885-3.83358.4407-4.60843.20930.10450.24860.2608-0.56780.18750.20610.0027-0.2335-0.28050.26990.0225-0.00470.27680.02040.24878.71482.442-15.267
52.08353.8155-1.02798.2091-3.35349.49380.3857-0.28510.08750.8909-0.2079-0.4046-0.79340.3986-0.09260.3271-0.01190.03070.3065-0.05610.28739.47471.76240.3926
64.00321.428-5.48242.0259-1.05026.6435-0.0751-0.67650.1474-0.09240.0298-0.40140.02680.57910.01550.2164-0.00990.0010.3054-0.00080.316926.2845-8.4689-6.4879
71.314-0.2794-0.0066.191.69551.40410.0133-0.1471-0.00750.0138-0.11460.20220.0717-0.10480.14020.156-0.01020.01450.22060.00980.15468.2323-17.6818-9.5468
85.74241.12581.08724.39511.00773.92610.05210.3659-0.3081-0.3071-0.04510.06310.1549-0.25650.03540.24450.01640.03710.234-0.03010.183812.4332-31.7004-19.0504
92.23341.82161.99948.73840.5715.80460.13270.0154-0.22620.50360.00930.39910.6343-0.4948-0.06880.2835-0.0247-0.02670.27090.06670.215915.953-31.1944-1.75
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 31 )A4 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 63 )A32 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 78 )A64 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 91 )A79 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 105 )A92 - 105
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 31 )B - C3 - 31
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 63 )B - C32 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 91 )B - C64 - 91
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 106 )B - C92 - 106

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