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- PDB-7qz7: Transcriptional regulator LmrR with bound daunomycin and with Trp... -

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Basic information

Entry
Database: PDB / ID: 7qz7
TitleTranscriptional regulator LmrR with bound daunomycin and with Trp-67 and Trp-96 replaced by 5,6,7-trifluoroTrp
ComponentsTranscriptional regulator, PadR-like familyTranscriptional regulation
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / PadR / Fluorinated tryptophan / daunomycin / pi-pi interactions
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DAUNOMYCIN / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7003
Polymers27,1732
Non-polymers5281
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-24 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.495, 35.091, 68.074
Angle α, β, γ (deg.)90.000, 98.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 108)
21(chain B and resid 4 through 108)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 108 / Label seq-ID: 4 - 108

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 4 through 108)AA
2(chain B and resid 4 through 108)BB

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Components

#1: Protein Transcriptional regulator, PadR-like family / Transcriptional regulation


Mass: 13586.316 Da / Num. of mol.: 2 / Mutation: W67 and W96 are replaced by 5,6,7-trifluoroTrp
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: Chemical ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN / Daunorubicin


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO10 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 2.3→33.71 Å / Num. obs: 10772 / % possible obs: 98.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 59.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.034 / Rrim(I) all: 0.059 / Net I/σ(I): 9.1 / Num. measured all: 30722 / Scaling rejects: 69
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
2.3-2.3830.865316710720.5090.5991.0561.198.9
8.91-33.712.60.0325312040.9970.0220.0392696.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3f8b


Resolution: 2.3→33.71 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 36.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2904 539 5.01 %
Rwork0.2245 10213 -
obs0.2285 10752 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.93 Å2 / Biso mean: 94.4184 Å2 / Biso min: 34.31 Å2
Refinement stepCycle: final / Resolution: 2.3→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 67 2 1762
Biso mean--119.07 65.17 -
Num. residues----204
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A962X-RAY DIFFRACTION3.89TORSIONAL
12B962X-RAY DIFFRACTION3.89TORSIONAL
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 (%)
2.3-2.530.3411260.2762549267599
2.53-2.90.36591310.30472508263998
2.9-3.650.33151410.26682532267398
3.65-33.710.25941410.18932624276599
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)
18.9828-1.9842-3.88716.0015-0.21042.59030.4150.3260.26130.0759-0.2406-0.1947-0.6629-1.4351-0.21530.36860.0287-0.0570.5554-0.03750.5407114.19725.80185.6538
25.9056-4.1605-2.31669.7296-1.37336.11080.27140.251-0.0233-0.0553-0.34-0.4782-0.10550.01650.02280.286-0.0869-0.01550.28860.00430.6555126.96994.99641.6394
38.1660.705-6.64330.0429-0.97219.14770.107-0.4144-1.48770.2553-0.7241-0.016-0.36950.33920.44860.9108-0.1289-0.18490.5660.07160.8645115.7955-5.579823.5143
43.6728-3.612-4.75954.20772.99838.66560.27640.2391-0.6305-0.9296-0.6814-0.3476-0.412-0.5510.22840.8108-0.0616-0.07610.76130.07390.5354115.50133.992328.6677
58.4964-1.55471.49183.60114.33196.8541-0.2671-1.00950.1710.42330.3249-0.0662-0.622-0.6273-0.1170.83010.1592-0.00760.8021-0.00270.534114.81525.005139.3803
65.9104-2.57253.48538.3352-0.58282.1919-1.4068-1.28350.52850.8515-0.2453-0.1727-1.2829-2.14321.76531.22720.508-0.29761.3677-0.32220.8604106.981313.807243.6106
76.2821-6.8137-5.0599.37495.673.9328-0.9034-0.0741-0.2180.45560.60860.224-0.0865-0.06850.32390.5401-0.066-0.08091.03480.06650.5999105.09165.093917.2953
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 82 )A47 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 109 )A83 - 109
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 23 )B3 - 23
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 59 )B24 - 59
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 82 )B60 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 108 )B83 - 108

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