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- PDB-6ejw: Tryptophan Repressor TrpR from E.coli wildtype with Indole-3-acet... -

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Basic information

Entry
Database: PDB / ID: 6ejw
TitleTryptophan Repressor TrpR from E.coli wildtype 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: 1.99 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 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model / struct_conn
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn

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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
C: Trp operon repressor
D: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,99111
Polymers53,7654
Non-polymers1,2267
Water3,351186
1
A: Trp operon repressor
B: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5836
Polymers26,8832
Non-polymers7014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-25 kcal/mol
Surface area11490 Å2
MethodPISA
2
C: Trp operon repressor
D: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4085
Polymers26,8832
Non-polymers5263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-30 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.310, 81.310, 72.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Trp operon repressor


Mass: 13441.283 Da / Num. of mol.: 4
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(DE3) (bacteria) / References: UniProt: P0A881
#2: Chemical
ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationMonochromator: DOUBLE-CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.99→44.928 Å / Num. obs: 32112 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.494 % / Biso Wilson estimate: 39.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.101 / Χ2: 1.03 / Net I/σ(I): 11.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.045.752.0710.9522380.4322.2793.7
2.04-2.16.4791.6761.3823090.5441.823100
2.1-2.166.2111.1382.0822380.6371.24299.9
2.16-2.226.1450.9772.5722070.7561.06999.8
2.22-2.36.6730.7763.3421030.8360.84299.9
2.3-2.386.8610.5444.720590.9150.589100
2.38-2.476.8960.4095.8820040.9540.443100
2.47-2.576.8840.3167.2318920.9720.342100
2.57-2.686.7280.2279.3418220.9820.247100
2.68-2.816.2820.20110.417460.9850.2299.9
2.81-2.976.6130.16212.6116710.9880.177100
2.97-3.157.010.11816.1315840.9930.12899.8
3.15-3.366.8170.08420.1514880.9960.092100
3.36-3.636.6040.06824.0713810.9970.07499.8
3.63-3.986.0580.05725.6812700.9970.06399.5
3.98-4.455.9750.04827.8811620.9980.05299.9
4.45-5.146.7240.04531.2810240.9990.04999.7
5.14-6.296.4770.04329.648600.9990.04799.2
6.29-8.95.9820.03932.446740.9990.04399.4
8.9-44.9286.5470.02536.8438010.02799

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.99 Å44.93 Å
Translation1.99 Å44.93 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: 1.99→44.928 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4
RfactorNum. reflection% reflection
Rfree0.2429 1606 5 %
Rwork0.1945 --
obs0.1969 32090 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.88 Å2 / Biso mean: 50.3555 Å2 / Biso min: 26.77 Å2
Refinement stepCycle: final / Resolution: 1.99→44.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 130 186 3564
Biso mean--50.56 51.45 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083492
X-RAY DIFFRACTIONf_angle_d0.9024728
X-RAY DIFFRACTIONf_chiral_restr0.048515
X-RAY DIFFRACTIONf_plane_restr0.005611
X-RAY DIFFRACTIONf_dihedral_angle_d10.7312926
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 (%)
1.9896-2.05380.36321390.30882647278695
2.0538-2.12720.29541460.260527582904100
2.1272-2.21240.27161450.241927702915100
2.2124-2.31310.28971460.226627602906100
2.3131-2.4350.28281460.209227762922100
2.435-2.58760.24081460.19527822928100
2.5876-2.78730.25291470.201927982945100
2.7873-3.06780.26291460.213727742920100
3.0678-3.51160.26771480.191928012949100
3.5116-4.42360.19861470.163727892936100
4.4236-44.93940.21571500.18072829297999
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)
18.6355.1236.2443.58185.07578.81880.7706-1.6731.25441.472-0.46481.10320.7533-1.1798-0.31220.86010.10350.16580.9839-0.16180.9645-74.18239.6891-15.3849
24.57195.6525-1.88438.0375-0.69226.49220.27590.0258-0.09470.213-0.1540.1401-0.0368-0.251-0.05330.29780.0652-0.00610.19360.04770.2762-61.07321.208-19.8605
35.66734.7111-0.71327.4543-1.61273.21560.1319-0.3140.19740.1736-0.15330.26180.0928-0.1535-0.06160.3298-0.0111-0.01830.3543-0.04230.3727-55.4921-23.4872-9.5286
42.08620.35951.13782.69433.7797.2721-0.02570.16780.0776-0.24840.0165-0.1624-0.21350.5247-0.02850.3322-0.04440.01140.3668-0.00390.4296-39.6717-20.7471-18.7418
53.3651-2.0822-2.18389.79-3.96034.8196-0.06831.24960.1733-2.7092-0.0954-1.77250.81150.70240.1390.8379-0.00260.14720.9033-0.04660.6668-36.1819-29.4433-36.1001
66.5831-2.53230.14027.47061.77476.752-0.34760.3091-0.0065-0.18740.35670.7247-0.6289-0.00790.03480.4626-0.0694-0.0670.42320.04610.3039-48.8013-21.6943-31.0631
78.2396-5.0011-1.94683.20880.80090.92780.3571-0.05370.887-0.4739-0.0686-0.347-0.29170.1018-0.21180.3929-0.082-0.0160.39240.00070.4579-34.676-18.2581-20.9994
82.61210.64562.29172.7534-1.30235.86120.0894-0.20560.0491-0.0459-0.06730.21680.1704-0.5889-0.0770.3160.02910.01570.4031-0.00420.459-49.6968-22.846-11.5656
97.3841-1.9215-1.48471.34522.22614.493-0.2864-0.3722-1.43942.39390.47571.74590.2347-0.69620.20350.9609-0.06570.27750.7090.24730.9184-50.5108-32.82225.0717
106.5082-1.5552-0.17339.0933-4.01853.16540.1753-0.27730.43630.4112-0.4574-0.4289-0.18070.28370.3180.2693-0.0584-0.04250.4045-0.07220.2597-41.1771-19.98640.8993
117.6417-3.0585-1.18174.64280.51552.4379-0.0944-0.23360.8251-0.02680.0415-0.2388-0.0744-0.14420.07650.34360.0177-0.0440.2917-0.00460.3584-63.514414.9097-30.143
122.48830.35513.17642.9123-1.11944.6950.03120.0922-0.1747-0.4024-0.004-0.11130.4289-0.0539-0.12650.35980.0470.02390.284-0.02660.3714-61.7478-0.5976-39.9746
139.8508-2.5076-7.69586.9241-2.27799.62070.3441.2825-1.5872-0.58850.37910.31110.6004-0.7325-0.52870.9977-0.0932-0.1190.8848-0.26310.8984-69.6577-5.0522-56.4208
142.82892.5569-3.63645.6263-4.42115.0528-0.0942-0.17520.04330.24770.05940.17450.189-0.65110.16940.5632-0.00290.00920.44880.0340.4771-71.88426.6478-50.8723
155.80080.01330.41785.94124.42625.8478-0.3740.98880.3212-1.78041.003-0.2539-0.58780.9472-0.29010.7943-0.09420.03230.52390.06290.4087-55.74410.0548-52.0162
165.61891.76530.00982.48621.66542.2004-0.13610.1828-0.7998-0.2350.284-0.8280.2292-0.0923-0.11460.44290.01880.03610.32620.01880.4126-58.5502-5.3397-41.3911
172.76890.1897-1.00613.0784-1.69136.9657-0.0834-0.10220.0676-0.08390.16990.2009-0.2635-0.5009-0.16110.37550.0266-0.01880.2169-0.0010.3718-63.94349.6029-32.2436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 64 through 78 )D64 - 78
2X-RAY DIFFRACTION2chain 'D' and (resid 79 through 105 )D79 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 5 through 31 )A5 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 63 )A32 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 78 )A64 - 78
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 105 )A79 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 31 )B5 - 31
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 63 )B32 - 63
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 78 )B64 - 78
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 105 )B79 - 105
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 32 )C5 - 32
12X-RAY DIFFRACTION12chain 'C' and (resid 33 through 63 )C33 - 63
13X-RAY DIFFRACTION13chain 'C' and (resid 64 through 78 )C64 - 78
14X-RAY DIFFRACTION14chain 'C' and (resid 79 through 90 )C79 - 90
15X-RAY DIFFRACTION15chain 'C' and (resid 91 through 105 )C91 - 105
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 31 )D5 - 31
17X-RAY DIFFRACTION17chain 'D' and (resid 32 through 63 )D32 - 63

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