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- PDB-7qz5: Transcriptional regulator LmrR with Trp-67 and Trp-96 replaced by... -

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Basic information

Entry
Database: PDB / ID: 7qz5
TitleTranscriptional regulator LmrR with Trp-67 and Trp-96 replaced by the unnatural amino acid 5-fluoroTrp
ComponentsTranscriptional regulator, PadR-like family
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / PadR / Fluorinated tryptophan
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 / metal ion binding / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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

Downloads & links

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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)28,6862
Polymers28,6862
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-19 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.624, 35.494, 70.914
Angle α, β, γ (deg.)90.000, 95.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 68 or resid 76 through 113))
21(chain B and resid 4 through 113)

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
11ILEILEGLYGLY(chain A and (resid 4 through 68 or resid 76 through 113))AA4 - 684 - 68
12ARGARGGLUGLU(chain A and (resid 4 through 68 or resid 76 through 113))AA76 - 11376 - 113
21ILEILESERSER(chain B and resid 4 through 113)BB4 - 1124 - 112

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Components

#1: Protein Transcriptional regulator, PadR-like family


Mass: 14343.235 Da / Num. of mol.: 2 / Mutation: W67 and W96 are replaced by 5-fluoro-Trp
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein solution: 6 mg/ml in 20 mM Tris-HCl, pH 8.0, 300 mM NaCl. Reservoir solution: 100 mM HEPES, pH 7.0, 200 mM NH4Cl, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.8→43.57 Å / Num. obs: 23803 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 40.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.022 / Rrim(I) all: 0.039 / Net I/σ(I): 8.3 / Num. measured all: 72652 / Scaling rejects: 1
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
1.8-1.8431.041401413260.4450.6861.2511.194.8
9.01-43.572.70.0315492000.9970.0230.03814.693

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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: 1.8→35.31 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1213 5.1 %
Rwork0.2184 22586 -
obs0.22 23799 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.88 Å2 / Biso mean: 60.2576 Å2 / Biso min: 27.04 Å2
Refinement stepCycle: final / Resolution: 1.8→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 44 1813
Biso mean---49.25 -
Num. residues----215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A999X-RAY DIFFRACTION5.863TORSIONAL
12B999X-RAY DIFFRACTION5.863TORSIONAL
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 (%)
1.8-1.870.43381290.42372442257197
1.87-1.960.34531220.32762516263899
1.96-2.060.26661410.2612456259799
2.06-2.190.25241400.24012520266099
2.19-2.360.24841610.24042491265299
2.36-2.60.26571090.22322523263299
2.6-2.980.27581480.23182520266899
2.98-3.750.25091410.21752518265999
3.75-35.310.21821220.19012600272298
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)
18.2001-0.9878-2.77234.06720.66.57980.24130.17250.29580.0836-0.28150.22340.1-0.9830.06450.23950.0008-0.02230.3405-0.05050.272511.83995.96125.4054
22.179-3.7750.8338.6863-4.6398.2858-0.10470.25560.9340.4483-0.0215-0.7974-0.68250.21440.04970.287-0.04380.03080.27610.00850.439823.257610.12626.4113
36.3581-0.9883-0.94417.0449-1.12742.00710.02920.7270.2309-1.1307-0.303-0.33070.5432-0.11130.1810.44970.04010.04810.25620.02440.355924.92381.306-3.7296
46.7034-0.102-7.15482.09960.95695.7506-0.48260.0422-0.78470.161-0.17650.56330.5606-0.28460.710.3785-0.00980.00450.3543-0.00990.473312.1345-6.268425.8206
55.3258-2.7561-1.09199.73621.87168.3425-0.3212-0.17150.02320.89360.45550.15850.0799-0.0999-0.09520.40030.0284-0.0710.3445-0.03440.372213.3191.745834.6008
64.4704-1.3179-0.91872.01460.41495.0363-0.1309-0.5870.53191.19050.0655-1.6061-0.47690.50560.10520.43450.0284-0.09850.4597-0.05030.583216.82566.337836.2565
72.25490.46891.9841.64930.39344.8237-1.1302-1.00690.5622.40331.21280.0751-0.0971-1.25190.24641.14950.4673-0.11950.6817-0.17550.45287.28313.448341.6867
80.4044-2.5499-1.83935.84196.26286.1172-0.4541-0.0212-0.4597-0.1508-0.53860.9126-0.2496-0.89630.90350.3767-0.0696-0.00050.7103-0.12920.58743.58412.969914.3835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 46 )A4 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 59 )A47 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 82 )A60 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 113 )A83 - 113
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 38 )B2 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 59 )B39 - 59
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 82 )B60 - 82
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 112 )B83 - 112

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