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- PDB-6f9k: Tryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan ... -

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Basic information

Entry
Database: PDB / ID: 6f9k
TitleTryptophan Repressor TrpR from E.coli with 5-methyl-L-tryptophan 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
5-methyl-L-tryptophan / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.399 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 from E.coli: A ligand binding study
Authors: Stiel, A.C. / Shanmugaratnam, S. / Hocker, B.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6999
Polymers13,4411
Non-polymers1,2578
Water1,18966
1
A: Trp operon repressor
hetero molecules

A: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,39718
Polymers26,8832
Non-polymers2,51516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_557-x,y,-z+21
Buried area7110 Å2
ΔGint-163 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.146, 53.146, 90.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Trp operon repressor


Mass: 13441.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A881
#2: Chemical
ChemComp-D0Q / 5-methyl-L-tryptophan


Type: L-peptide linking / Mass: 218.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Citric acid pH3.5, 2.4M Ammonium sulfate, pH4.0 cryo: +25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→20.88 Å / Num. all: 26306 / Num. obs: 26294 / % possible obs: 99.5 % / Redundancy: 8.475 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.081 / Χ2: 1.049 / Net I/σ(I): 14.74 / Num. measured all: 222787 / Scaling rejects: 49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.448.6095.0040.3816142190318750.1785.32498.5
1.44-1.488.6753.3840.6316058186718510.3353.59999.1
1.48-1.528.6062.3270.9415370181217860.5832.47798.6
1.52-1.568.2481.8381.214491176917570.5911.96299.3
1.56-1.627.6181.3911.4912958170417010.7341.49499.8
1.62-1.679.0461.1172.1115070166816660.8581.18599.9
1.67-1.749.0290.8142.8514392159915940.8960.86499.7
1.74-1.818.9990.6483.5713876154715420.9230.68799.7
1.81-1.898.860.4355.2113263150114970.9640.46299.7
1.89-1.988.7290.3117.1912413142314220.9820.33199.9
1.98-2.098.4730.19611.2811506136413580.9910.20999.6
2.09-2.217.6640.12915.459925130412950.9960.13899.3
2.21-2.378.2670.09121.9310011121112110.9980.097100
2.37-2.568.9340.06929.0110230114511450.9990.073100
2.56-2.88.7990.05137.169345106210620.9990.054100
2.8-3.138.4960.0446.0982509729710.9990.04299.9
3.13-3.617.8810.02758.5167388558550.9990.028100
3.61-4.436.8570.02264.9951157517460.9990.02499.3
4.43-6.268.520.01974.84506159459410.02100
6.26-20.887.1470.0270.78257336736010.02198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.69 Å45.87 Å
Translation4.69 Å45.87 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tro

1tro


Resolution: 1.399→20.88 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 1315 5 %
Rwork0.1933 24979 -
obs0.194 26294 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.4 Å2 / Biso mean: 43.3844 Å2 / Biso min: 18.1 Å2
Refinement stepCycle: final / Resolution: 1.399→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 108 66 1028
Biso mean--56.08 45.1 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009971
X-RAY DIFFRACTIONf_angle_d0.9591322
X-RAY DIFFRACTIONf_chiral_restr0.062139
X-RAY DIFFRACTIONf_plane_restr0.007167
X-RAY DIFFRACTIONf_dihedral_angle_d23.781362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3995-1.45550.44631420.46032693283599
1.4555-1.52170.3531420.36352697283999
1.5217-1.60190.33661430.307227232866100
1.6019-1.70230.27181440.245627442888100
1.7023-1.83360.23231460.212127602906100
1.8336-2.0180.21921450.190727562901100
2.018-2.30970.18231470.162227842931100
2.3097-2.90870.18331480.169528302978100
2.9087-20.88230.1841580.176629923150100
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)
11.0037-1.17341.28022.1154-2.32262.61690.13180.36410.1215-0.1723-0.3985-0.1828-0.1010.34130.31140.2222-0.04220.00320.23810.02540.250110.620116.692585.8644
21.40790.68510.48671.2588-2.1957.30160.0305-0.06590.10990.0838-0.03880.0132-0.2104-0.4014-0.00590.17190.0375-0.00050.1856-0.03530.1973-5.799416.420194.4535
36.09135.31813.70244.64313.23682.86480.294-0.54330.06911.1788-0.79590.87520.8782-1.07820.47030.4849-0.13180.04770.5590.02080.4249-10.79599.3418110.8982
41.8123-1.7983-0.28426.9180.85262.7046-0.0278-0.12990.0833-0.04620.05260.0013-0.1204-0.0517-0.03050.1968-0.0426-0.01960.2457-0.02260.1750.906119.3548107.8584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 32 )A3 - 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 108 )A79 - 108

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