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- PDB-3f8b: Crystal structure of the multidrug binding transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 3f8b
TitleCrystal structure of the multidrug binding transcriptional regulator LmrR in drug free state
ComponentsTranscriptional regulator, PadR-like family
KeywordsTRANSCRIPTION REGULATOR / Winged helix turn helix
Function / homologyTranscription 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 / Transcriptional regulator, PadR-like family
Function and homology information
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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 / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water1,49583
1
A: Transcriptional regulator, PadR-like family

A: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2190 Å2
ΔGint-21 kcal/mol
Surface area12840 Å2
MethodPISA
2
B: Transcriptional regulator, PadR-like family

B: Transcriptional regulator, PadR-like family


Theoretical massNumber of molelcules
Total (without water)26,9572
Polymers26,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
Buried area2300 Å2
ΔGint-16 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.669, 52.695, 174.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 13478.371 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 1500, 0.1M propionic acid, cacodylate, Bis-Tris propane (PCB buffer), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→87.499 Å / Num. all: 14971 / Num. obs: 14971 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 4.414
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.117.80.5031.41675121480.50399.3
2.11-2.247.90.3342.11607920260.33499.5
2.24-2.397.90.2812.51513119210.28199.6
2.39-2.587.90.2223.21413417970.22299.7
2.58-2.837.80.1783.91275316330.17899.8
2.83-3.167.70.1275.21178315220.12799.9
3.16-3.657.50.0956.71013513440.09599.9
3.65-4.477.40.0738858211610.073100
4.47-6.3270.0597.663519020.05999.5
6.32-35.016.70.04910.737095520.04999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.33 Å
Translation2.5 Å23.33 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ESH, 1YYV, 1XMA

2esh

1yyv

1xma


Resolution: 2→87.37 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU B: 9.879 / SU ML: 0.146 / SU R Cruickshank DPI: 0.223 / SU Rfree: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.223 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: AUTHOR CHECKED USING MOLPROBITY AND IN COOT FOR TORSION ANGLES OUTSIDE AND ALL RESIDUES ARE WITHIN THE ALLOWED CONFORMATIONS. THERE ARE NO OUTLIERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 756 5 %RANDOM
Rwork0.219 ---
all0.221 14971 --
obs0.221 14961 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 38.35 Å2 / Biso mean: 15.38 Å2 / Biso min: 2.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2--0.6 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2→87.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 83 1775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221717
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9542302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.6275203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.14424.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.32715335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4951514
X-RAY DIFFRACTIONr_chiral_restr0.1230.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021274
X-RAY DIFFRACTIONr_nbd_refined0.2160.2745
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.222
X-RAY DIFFRACTIONr_mcbond_it0.7191.51068
X-RAY DIFFRACTIONr_mcangle_it1.12521624
X-RAY DIFFRACTIONr_scbond_it1.7933776
X-RAY DIFFRACTIONr_scangle_it2.7654.5678
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 50 -
Rwork0.218 1045 -
all-1095 -
obs--99.18 %
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)
11.46256.2263-0.929326.7949-1.600819.92610.0874-0.1150.28620.5849-0.2696-1.25510.17361.37190.18220.06290.0278-0.06190.2509-0.03230.281926.11646.5983-4.2209
22.9415-2.6545-0.64553.43810.41581.4402-0.01560.03330.19940.0513-0.0872-0.0652-0.184-0.02360.10280.073-0.0201-0.00340.0791-0.03130.074117.6775-0.0568-16.9532
311.8339-4.16091.43094.263-0.67211.15380.1467-0.28460.54130.1578-0.12210.1779-0.1578-0.1389-0.02460.04490.00710.06690.0813-0.05970.138323.73135.2708-16.0114
43.30911.1395-1.1313.23060.09085.80520.01850.08320.1784-0.11090.0668-0.1926-0.14130.2063-0.08530.0560.00780.00370.035-0.01960.10325.5935-9.9834-18.5617
53.6876-4.9288-6.81377.01539.074512.5923-0.01160.2195-0.1168-0.1832-0.19480.148-0.0233-0.40650.20640.098-0.04530.00130.1393-0.01640.094411.9032-5.24255.0518
64.07093.28591.36265.3184-5.685317.7233-0.3879-0.17021.0082-0.49280.7443-0.4393-1.90610.5293-0.35630.50580.0820.21230.2213-0.02720.367452.49214.3387-40.1625
73.4019-1.6784-2.01752.62231.48671.89650.09690.2015-0.10840.1247-0.1214-0.06270.13320.04110.02460.0645-0.0066-0.00750.0599-0.01070.042947.7016-3.6097-26.3891
88.4887-1.09341.90832.2852-0.0611.6055-0.12660.0984-0.1133-0.06670.00720.0084-0.00710.00330.11940.11310.01960.02810.0665-0.02010.054946.89796.4806-28.4406
92.4380.54940.0312.97682.55449.84480.0279-0.06740.21740.2374-0.10010.10740.2913-0.25520.07220.0653-0.04870.02020.05030.01410.095936.56470.2117-24.2947
1012.3987-0.6186-7.36865.71144.972514.28430.1228-0.4379-0.61250.1489-0.2088-0.07780.16730.00210.08590.0619-0.0231-0.03650.08090.10410.025543.4583-10.5306-53.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 11
2X-RAY DIFFRACTION2A12 - 40
3X-RAY DIFFRACTION3A41 - 55
4X-RAY DIFFRACTION4A56 - 88
5X-RAY DIFFRACTION5A89 - 109
6X-RAY DIFFRACTION6B6 - 11
7X-RAY DIFFRACTION7B12 - 42
8X-RAY DIFFRACTION8B43 - 61
9X-RAY DIFFRACTION9B62 - 95
10X-RAY DIFFRACTION10B96 - 109

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