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- PDB-6f7g: Tryptophan Repressor TrpR from E.coli with 5-Methyltryptamine -

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Basic information

Entry
Database: PDB / ID: 6f7g
TitleTryptophan Repressor TrpR from E.coli with 5-Methyltryptamine
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
2-(5-methyl-1~{H}-indol-3-yl)ethanamine / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.656 Å
AuthorsStiel, A.C. / Shanmugaratnam, S. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHO 4022/2-3 Germany
CitationJournal: To Be Published
Title: Tryptophan Repressor TrpR: A ligand specificity study
Authors: Stiel, A.C. / Shanmugaratnam, S. / Hocker, B.
History
DepositionDec 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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
C: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0244
Polymers23,6752
Non-polymers3482
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-35 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.349, 55.548, 66.992
Angle α, β, γ (deg.)90.000, 98.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trp operon repressor


Mass: 11837.562 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-CVW / 2-(5-methyl-1~{H}-indol-3-yl)ethanamine


Mass: 174.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 Sodium Chloride 0.1 M HEPES pH7.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.656→34.931 Å / Num. obs: 29831 / % possible obs: 97.3 % / Redundancy: 6.166 % / Biso Wilson estimate: 15.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 0.997 / Net I/σ(I): 15.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.656-1.75.9090.314.0619350.9610.33984.7
1.7-1.756.6550.3015.1321770.9670.32699.9
1.75-1.86.6640.2335.8521370.9750.25399.6
1.8-1.856.4270.2266.5120930.9760.24699.5
1.85-1.914.8490.2237.2118380.9840.25491.3
1.91-1.985.0840.1988.9717810.9870.22492.8
1.98-2.056.3930.14911.0918660.9870.16399.4
2.05-2.145.5450.11813.4417900.9850.13298.7
2.14-2.236.4620.09616.2917370.9920.10498.4
2.23-2.345.7560.08717.4916000.9870.09897.5
2.34-2.476.730.07620.3115580.9960.08399.8
2.47-2.626.3350.07221.1314970.9960.07899.8
2.62-2.85.7880.06522.3114150.9960.07199
2.8-3.027.1620.06226.2613040.9970.06799.9
3.02-3.316.9780.05628.712050.9970.061100
3.31-3.75.8920.05727.9911030.9960.06399.2
3.7-4.285.8820.05429.219660.9960.05999.3
4.28-5.245.9990.04729.998140.9970.05198.9
5.24-7.417.0650.04731.956510.9980.05100
7.41-34.9316.8930.04533.383640.9980.04898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.66 Å34.93 Å
Translation1.66 Å34.93 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tro

1tro


Resolution: 1.656→34.931 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.2255 1481 4.99 %
Rwork0.185 --
obs0.187 29658 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.86 Å2 / Biso mean: 25.4834 Å2 / Biso min: 6.22 Å2
Refinement stepCycle: final / Resolution: 1.656→34.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 26 346 1992
Biso mean--13.93 33.64 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061674
X-RAY DIFFRACTIONf_angle_d0.7722261
X-RAY DIFFRACTIONf_chiral_restr0.047254
X-RAY DIFFRACTIONf_plane_restr0.004291
X-RAY DIFFRACTIONf_dihedral_angle_d5.8051235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.656-1.70940.30581220.26662309243187
1.7094-1.77050.29131390.241926462785100
1.7705-1.84130.27841360.213625842720100
1.8413-1.92510.36621220.32112319244188
1.9251-2.02660.2921340.23112540267496
2.0266-2.15360.20211350.2142595273098
2.1536-2.31980.23021320.18292545267796
2.3198-2.55320.18511400.161826472787100
2.5532-2.92250.22231390.165326452784100
2.9225-3.68140.21271390.15226362775100
3.6814-34.93890.18381430.15832711285499
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)
14.5754-2.8314.3651.9049-2.62584.27010.08880.0782-0.2272-0.05550.06190.1708-0.0075-0.0085-0.0830.1043-0.00970.02640.1204-0.0070.1687-9.01484.646267.5053
21.3252-0.4656-0.79111.01020.63141.42660.0164-0.39990.13730.1515-0.02070.0981-0.08890.0447-0.00280.1523-0.00660.02230.1711-0.06320.1277-2.456411.839184.2043
30.6786-0.1211-0.44851.02950.19351.52990.0351-0.11420.20960.47650.13760.1209-0.2355-0.2644-0.0670.52270.04290.21280.6658-0.28880.481-12.624321.301496.9182
43.7990.18330.01424.88650.13192.4979-0.0319-0.3830.16110.4715-0.02120.66340.0021-0.57520.01090.2136-0.01860.11180.3488-0.02740.2707-15.97717.829789.3495
54.18561.17741.00647.12160.4565.30150.1153-0.6510.15930.5653-0.0943-0.4835-0.05830.2301-0.04260.1435-0.00510.03720.2333-0.02620.15550.16148.309188.2645
62.62191.0118-2.05331.3195-1.0453.27450.05450.09140.2677-0.04820.07570.1862-0.0873-0.1672-0.10010.0987-0.0024-0.03350.0682-0.01320.1256-3.799510.912166.4283
71.4503-0.39420.71731.8616-0.72021.81840.00420.0426-0.0072-0.1555-0.0642-0.1135-0.06370.24570.05470.0928-0.00470.00980.0910.00220.12578.48938.746466.7809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )A4 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 63 )A33 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 78 )A64 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 106 )A79 - 106
5X-RAY DIFFRACTION5chain 'C' and (resid 9 through 32 )C9 - 32
6X-RAY DIFFRACTION6chain 'C' and (resid 33 through 78 )C33 - 78
7X-RAY DIFFRACTION7chain 'C' and (resid 79 through 106 )C79 - 106

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