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- PDB-7qz8: Transcriptional regulator LmrR with bound daunomycin and with Trp... -

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Basic information

Entry
Database: PDB / ID: 7qz8
TitleTranscriptional regulator LmrR with bound daunomycin and with Trp-67 and Trp-96 replaced by the unnatural amino acid 5,6-difluoroTrp
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)29,2863
Polymers28,7582
Non-polymers5281
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-23 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.146, 35.744, 71.154
Angle α, β, γ (deg.)90.000, 97.690, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 66 or resid 77 through 112))
21(chain B and resid 5 through 112)

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
11PROPROTYRTYR(chain A and (resid 5 through 66 or resid 77 through 112))AA5 - 665 - 66
12LYSLYSSERSER(chain A and (resid 5 through 66 or resid 77 through 112))AA77 - 11277 - 112
21PROPROSERSER(chain B and resid 5 through 112)BB5 - 1125 - 112

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Components

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


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
#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.: 11 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→70.51 Å / Num. obs: 14279 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 57.12 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.036 / Rrim(I) all: 0.063 / Net I/σ(I): 8.7 / Num. measured all: 44105 / Scaling rejects: 246
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
2.15-2.213.11.132361811780.4310.7711.3760.799
9.12-70.512.70.0445432020.9530.0370.05823.695.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8B

3f8b


Resolution: 2.3→70.51 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3172 581 4.98 %
Rwork0.2408 11086 -
obs0.2443 11667 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.37 Å2 / Biso mean: 79.9476 Å2 / Biso min: 37.63 Å2
Refinement stepCycle: final / Resolution: 2.3→70.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 66 11 1780
Biso mean--100.57 57.36 -
Num. residues----206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A960X-RAY DIFFRACTION6.369TORSIONAL
12B960X-RAY DIFFRACTION6.369TORSIONAL
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 (%)
2.3-2.530.32741480.29232713286198
2.53-2.90.34581640.31482747291199
2.9-3.650.38641380.282763290199
3.65-70.510.27171310.20422863299498
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)
17.6224-0.0768-2.57199.426-2.37246.12060.2921-0.79240.34770.1768-0.34030.5399-0.909-0.51790.11220.4205-0.0369-0.01290.5737-0.11020.5113.90775.97411.3273
24.8558-1.2972-1.66523.52610.89535.19240.27491.10820.0484-0.5238-0.43810.3049-0.2721-1.16660.2060.46240.1001-0.08370.5948-0.03250.439910.57076.1957-0.264
34.4306-1.7309-0.90015.2483-2.1265.97890.00860.18451.27140.3628-0.2419-0.7924-0.61820.25970.20540.4426-0.0038-0.03910.39560.04190.50523.295610.44576.2366
47.7438-4.07121.79714.3341-1.04189.9470.39440.62230.105-0.7109-0.4877-0.48190.88170.2210.04470.46440.01420.03530.34480.0030.576625.79531.8539-1.8948
52.05310.2348-1.98550.01530.19942.1323-0.6056-0.048-1.95730.1314-0.72770.340.125-0.04671.42450.68890.05440.11420.5331-0.02590.770912.145-5.63524.85
63.9345-3.3681-0.02116.63633.70353.28480.06460.1241-0.0063-0.5439-0.0713-0.7521-0.89370.66910.06930.47490.00120.02690.54030.00470.68513.34193.869228.9106
74.2199-2.4211-3.37458.64793.29695.7998-1.2958-0.9156-0.58352.45870.733-0.16780.78590.61910.36850.97280.2824-0.06010.71060.07550.595211.8501-0.661540.3867
87.2471-0.5817-0.1865.23061.05198.0963-0.7063-1.0550.46561.99430.4461-1.5236-1.25360.30190.10471.01880.1875-0.18710.6075-0.15130.71859.598213.973438.4832
90.6629-1.7937-2.40493.23934.4645.9901-0.44690.0748-0.45250.0943-0.39520.84370.2518-0.64450.7990.4751-0.0703-0.0180.84330.01250.7053.25923.707914.6858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 23 )A5 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )A24 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 59 )A47 - 59
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 82 )A60 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 112 )A83 - 112
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 23 )B3 - 23
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 46 )B24 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 82 )B47 - 82
9X-RAY DIFFRACTION9chain 'B' and (resid 83 through 112 )B83 - 112

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