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- PDB-7qz6: Transcriptional regulator LmrR with bound daunomycin and with Trp... -

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Basic information

Entry
Database: PDB / ID: 7qz6
TitleTranscriptional regulator LmrR with bound daunomycin and with Trp-67 and Trp-96 replaced by 5-fluoroTrp
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: 2.15 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2143
Polymers28,6862
Non-polymers5281
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-22 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.157, 35.382, 67.787
Angle α, β, γ (deg.)90.000, 97.310, 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 112))
21(chain B and (resid 5 through 68 or resid 74 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
11PROPROGLYGLY(chain A and (resid 5 through 68 or resid 74 through 112))AA5 - 685 - 68
12GLYGLYSERSER(chain A and (resid 5 through 68 or resid 74 through 112))AA74 - 11274 - 112
21PROPROGLYGLY(chain B and (resid 5 through 68 or resid 74 through 112))BB5 - 685 - 68
22GLYGLYSERSER(chain B and (resid 5 through 68 or resid 74 through 112))BB74 - 11274 - 112

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Components

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


Mass: 14343.235 Da / Num. of mol.: 2 / Mutation: W67 and W96 are replaced by 5-fluoroTrp
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.: 22 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
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: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→43.47 Å / Num. obs: 13450 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.025 / Rrim(I) all: 0.045 / Net I/σ(I): 14.1 / Num. measured all: 45664 / Scaling rejects: 13
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
2.15-2.223.40.638403711740.480.4010.7561.799.7
8.86-43.4730.0326272120.9980.0220.03939.598.6

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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: 2.15→43.47 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 696 5.18 %
Rwork0.2258 12746 -
obs0.2289 13442 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.52 Å2 / Biso mean: 90.0857 Å2 / Biso min: 29.77 Å2
Refinement stepCycle: final / Resolution: 2.15→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 66 22 1800
Biso mean--121.47 60.68 -
Num. residues----208
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1018X-RAY DIFFRACTION5.355TORSIONAL
12B1018X-RAY DIFFRACTION5.355TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.320.39551390.349525302669100
2.32-2.550.33191450.29272504264999
2.55-2.920.35571140.293925602674100
2.92-3.680.27121450.25222530267599
3.68-43.470.26571530.18382622277599

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