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

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Basic information

Entry
Database: PDB / ID: 6elf
TitleTryptophan Repressor TrpR from E.coli variant M42F T44L T81I 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: 1.832 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)27,4654
Polymers27,1152
Non-polymers3502
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-29 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.960, 63.410, 64.820
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(DE3) (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5 12 % PEG 20000

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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: May 16, 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: 1.83→34.969 Å / Num. obs: 20421 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.535 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.098 / Χ2: 1.006 / Net I/σ(I): 17.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.83-1.8811.142.1861.2114210.762.29295.1
1.88-1.9311.5890.8453.1314620.860.88599.7
1.93-1.9913.2520.7773.7214040.9030.809100
1.99-2.0513.4430.4885.7413680.9580.507100
2.05-2.1213.5080.3598.3313540.9720.373100
2.12-2.1913.5360.30110.212920.9870.31399.9
2.19-2.2713.4160.22113.6912450.9890.2399.9
2.27-2.3713.2370.21214.2112010.9910.221100
2.37-2.4713.0110.16816.6911510.9950.17499.9
2.47-2.5912.2620.15518.311220.9930.16199.7
2.59-2.7311.0710.12120.4810420.9960.12799.7
2.73-2.912.9930.10424.5510050.9960.10899.9
2.9-3.113.3020.08229.419500.9980.085100
3.1-3.3412.9310.0733.278740.9990.072100
3.34-3.6612.2220.05837.628270.9980.06199.6
3.66-4.111.480.05538.697430.9980.05799.9
4.1-4.7310.8010.0539.786690.9990.05399.9
4.73-5.7910.4150.04839.065660.9990.0599.3
5.79-8.1912.7920.04543.584560.9990.046100
8.19-34.96911.0520.05243.492690.9970.05598.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.87 Å34.97 Å
Translation5.87 Å34.97 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: 1.832→34.969 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2167 1021 5 %
Rwork0.1773 --
obs0.1792 20417 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.12 Å2 / Biso mean: 36.0587 Å2 / Biso min: 15.1 Å2
Refinement stepCycle: final / Resolution: 1.832→34.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 26 155 1882
Biso mean--31.31 42.35 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131757
X-RAY DIFFRACTIONf_angle_d1.2022375
X-RAY DIFFRACTIONf_chiral_restr0.076261
X-RAY DIFFRACTIONf_plane_restr0.009309
X-RAY DIFFRACTIONf_dihedral_angle_d6.2021069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8322-1.92880.36451400.33512673281397
1.9288-2.04960.28211430.239527222865100
2.0496-2.20780.2571460.185327572903100
2.2078-2.430.22141440.167427452889100
2.43-2.78140.23191460.18127642910100
2.7814-3.50380.20791470.177828052952100
3.5038-34.97550.18471550.153329303085100
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)
14.4374-0.63535.20320.0605-0.64065.5174-0.02880.29870.29980.0492-0.0735-0.26540.07160.2896-0.15080.23020.0174-0.0120.22740.00450.233154.092112.52541.3921
20.82110.19120.29055.97151.19122.16670.0085-0.00520.24230.1938-0.02620.3351-0.1948-0.03550.04540.15530.01870.00190.2194-0.00840.206339.010229.491741.856
36.4561-0.9677-6.89190.02350.52416.71030.00830.27940.22810.05110.03170.2101-0.0321-0.2517-0.06060.22950.00680.00290.2229-0.02690.258228.706223.071639.0647
40.94210.3883-0.52774.7101-3.1333.61250.0807-0.1775-0.1350.274-0.285-0.26720.02860.24350.29470.1849-0.0022-0.02230.27880.02090.190547.30699.095145.1227
54.43-0.1081-1.00383.5652-1.58442.0229-0.04310.3554-0.1774-0.17020.16530.25050.6062-0.4933-0.05710.1823-0.0158-0.00730.18890.00690.184437.61761.176440.9307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 31 )B2 - 31
2X-RAY DIFFRACTION2chain 'B' and (resid 32 through 105 )B32 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 31 )A2 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 78 )A32 - 78
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 106 )A79 - 106

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