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- PDB-7qz9: Transcriptional regulator LmrR with Trp-67 and Trp-96 replaced by... -

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Basic information

Entry
Database: PDB / ID: 7qz9
TitleTranscriptional regulator LmrR with Trp-67 and Trp-96 replaced by the unnatural amino acid 5,6-difluoroTrp
ComponentsTranscriptional regulator, PadR-like family
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / PadR / fluorinated tryptophan / daunomycin / pi-pi interactions
Function / homology: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsThunnissen, A.M.W.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: The Role of Tryptophan in pi Interactions in Proteins: An Experimental Approach.
Authors: Shao, J. / Kuiper, B.P. / Thunnissen, A.W.H. / Cool, R.H. / Zhou, L. / Huang, C. / Dijkstra, B.W. / Broos, J.
History
DepositionJan 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, PadR-like family
B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)28,7582
Polymers28,7582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-21 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.377, 34.969, 68.107
Angle α, β, γ (deg.)90.000, 97.540, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 68 or resid 74 through 110))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLY(chain A and (resid 5 through 68 or resid 74 through 110))AA5 - 685 - 68
12GLYGLYLYSLYS(chain A and (resid 5 through 68 or resid 74 through 110))AA74 - 11074 - 110
21PROPROLYSLYSchain BBB5 - 1105 - 110

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14379.216 Da / Num. of mol.: 2 / Mutation: W67 and W96 are replaced by 5,6-difluoroTrp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus cremoris (lactic acid bacteria)
Strain: MG1363 / Gene: llmg_0323 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RI36
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: Protein solution: 6 mg/ml in 20 mM Tris-HCl, pH 8.0, 300 mM NaCl. Reservoir solution: 100 mM SPG buffer, pH 6.1, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91165 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 2.31→43.39 Å / Num. obs: 10549 / % possible obs: 97.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 9 / Num. measured all: 36134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.393.51.463352610010.4150.8951.7190.695.1
8.93-43.392.90.0165821990.9990.0110.0228.796.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8B

3f8b


Resolution: 2.31→43.39 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 37.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 512 4.85 %
Rwork0.2292 10034 -
obs0.2324 10546 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.71 Å2 / Biso mean: 92.91 Å2 / Biso min: 40.79 Å2
Refinement stepCycle: final / Resolution: 2.31→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 0 0 1705
Num. residues----206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A974X-RAY DIFFRACTION10.222TORSIONAL
12B974X-RAY DIFFRACTION10.222TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.540.35131180.30242461257996
2.54-2.910.36161170.30582504262198
2.91-3.660.39561390.27222499263898
3.66-43.390.24211380.19452570270897
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)
11.6774-0.2950.51710.6116-0.73362.7442-0.19790.021-0.0276-0.21960.21650.1313-0.13690.5789-0.00030.7899-0.014-0.0220.78950.02520.7351-12.838617.57792.642
23.2686-0.1337-1.85411.41680.43483.03180.047-0.084-0.1351-0.2498-0.17190.20940.0040.44890.00040.53370.0558-0.03880.47470.0760.5575-20.708113.848924.0557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 112 )A4 - 112
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 110 )B5 - 110

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