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- PDB-3f8c: Crystal structure of multidrug binding transcriptional regulator ... -

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Basic information

Entry
Database: PDB / ID: 3f8c
TitleCrystal structure of multidrug binding transcriptional regulator LmrR complexed with Hoechst 33342
ComponentsTranscriptional regulator, PadR-like family
KeywordsTRANSCRIPTION REGULATOR / Winged helix turn helix
Function / homology
Function and homology information


: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HT1 / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMadoori, P.K. / Agustiandari, H. / Driessen, A.J.M. / Thunnissen, A.-M.W.H.
CitationJournal: Embo J. / Year: 2009
Title: Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.
Authors: Madoori, P.K. / Agustiandari, H. / Driessen, A.J. / Thunnissen, A.M.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2172
Polymers14,7651
Non-polymers4531
Water46826
1
A: Transcriptional regulator, PadR-like family
hetero molecules

A: Transcriptional regulator, PadR-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4354
Polymers29,5302
Non-polymers9052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4850 Å2
ΔGint-23 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.93, 34.93, 197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 14764.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Strain: MG1363 / Gene: lmrR / Plasmid: pNSC8048 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: A2RI36
#2: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342


Mass: 452.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.55 % / Mosaicity: 0.49 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25% PEG 1500, 0.1M succinic acid/phosphate/glycine (SPG buffer), pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→49.27 Å / Num. all: 6957 / Num. obs: 6957 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.052
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.22 / Num. unique all: 969 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.28 Å
Translation2.5 Å49.28 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.7data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8B

3f8b


Resolution: 2.2→49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.813 / SU B: 13.411 / SU ML: 0.154 / SU R Cruickshank DPI: 0.262 / SU Rfree: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 327 4.8 %RANDOM
Rwork0.209 ---
all0.212 6874 --
obs0.212 6874 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 21.644 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å2-0 Å2
2--0.8 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 34 26 910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022901
X-RAY DIFFRACTIONr_angle_refined_deg0.9072.0141212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19224.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11415170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.187157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02669
X-RAY DIFFRACTIONr_mcbond_it3.8632507
X-RAY DIFFRACTIONr_mcangle_it5.5333814
X-RAY DIFFRACTIONr_scbond_it5.3012394
X-RAY DIFFRACTIONr_scangle_it7.9073398
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 327 -
Rwork0.209 464 -
all-481 -
obs-6547 100 %
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)
19.04162.6669-0.027717.8441-10.850823.07610.1216-0.7196-0.8070.2964-0.0995-0.17321.3198-0.0817-0.02210.1426-0.0167-0.00060.1512-0.03040.1692-0.6921-7.8828-6.4288
27.3168-0.88855.91746.8319-1.25256.62510.20560.4877-0.3727-0.3325-0.0284-0.06310.16650.7894-0.17720.0724-0.00530.05370.21860.01440.10744.7741-4.9889-19.3974
35.9538-3.68953.56710.55430.76756.1425-0.0070.18770.0474-0.3557-0.1166-0.08010.17210.27390.12360.128-0.0485-0.00250.1701-0.03980.2062-8.5573-5.7744-22.3984
40.72110.3313.06441.74122.372915.8953-0.1980.01660.1384-0.0440.0765-0.0044-0.78260.34530.12140.1769-0.0330.01510.13070.02020.2497-4.29075.2289-5.8455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 21
2X-RAY DIFFRACTION2A22 - 48
3X-RAY DIFFRACTION3A49 - 76
4X-RAY DIFFRACTION4A77 - 109

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