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- PDB-4zzd: CRYSTAL STRUCTURE OF MULTIDRUG RESISTANCE REGULATOR LMRR BOUND TO... -

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Basic information

Entry
Database: PDB / ID: 4zzd
TitleCRYSTAL STRUCTURE OF MULTIDRUG RESISTANCE REGULATOR LMRR BOUND TO RIBOFLAVIN
ComponentsTRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY
KeywordsTRANSCRIPTION / WINGED HELIX TURN HELIX / TRANSCRIPTION REGULATOR / MULTIDRUG BINDING / INTRACELLULAR
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
RIBOFLAVIN / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å
AuthorsMadoori, P.K. / Thunnissen, A.-M.W.H.
CitationJournal: Plos One / Year: 2015
Title: Binding of the Lactococcal Drug Dependent Transcriptional Regulator LmrR to Its Ligands and Responsive Promoter Regions.
Authors: van der Berg, J.P. / Madoori, P.K. / Komarudin, A.G. / Thunnissen, A.M. / Driessen, A.J.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8552
Polymers13,4781
Non-polymers3761
Water27015
1
A: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7094
Polymers26,9572
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3960 Å2
ΔGint-25 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.215, 35.215, 179.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-201-

RBF

21A-201-

RBF

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR, PADR-LIKE FAMILY


Mass: 13478.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria)
Gene: llmg_0323 / Plasmid: PNSC8048
Production host: Lactococcus lactis subsp. cremoris NZ9000 (lactic acid bacteria)
References: UniProt: A2RI36
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M TRIS-HCL, 17% PEG 2000 MME, 0.2M TRI-METHYLAMINE N-OXIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.351→34.5 Å / Num. obs: 5144 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 2.35→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.351→30.36 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.269 237 4.61 %Random selection
Rwork0.206 ---
obs0.21 5144 97.7 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.06 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5871 Å20 Å2-0 Å2
2--0.5871 Å20 Å2
3----1.1742 Å2
Refinement stepCycle: LAST / Resolution: 2.351→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 27 15 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008879
X-RAY DIFFRACTIONf_angle_d1.0131187
X-RAY DIFFRACTIONf_dihedral_angle_d19.505324
X-RAY DIFFRACTIONf_chiral_restr0.073126
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.351-2.9610.36571150.22732361X-RAY DIFFRACTION98
2.961-30.36380.23861220.19882546X-RAY DIFFRACTION98
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)
13.862-3.58083.35776.7373-3.2643.72110.19460.26640.2345-0.5469-0.09120.35230.5203-0.1127-0.19810.3597-0.068-0.03490.2560.07270.19570.77251.043399.2036
24.8452-1.8109-0.57784.3785-1.67533.9027-0.0808-0.30550.54530.37050.4130.6763-0.8846-0.3293-0.03070.29680.0351-0.07760.15650.01050.31391.28536.4915109.7256
34.1773-2.3329-1.7482.64690.30995.8121-0.07760.0806-0.23430.02730.15360.5775-0.2651-0.4861-0.0920.2027-0.0423-0.04040.10750.08720.2239-3.3601-6.982105.9624
40.9526-0.0521-0.33443.6952-0.33761.9028-0.0259-0.2405-0.14530.30560.10430.0883-0.0071-0.0380.32560.15820.0299-0.01580.19570.26960.19785.6869-9.0313111.9564
51.056-0.6650.27863.5396-3.54655.1442-0.5405-0.10110.32670.0467-0.3272-0.8307-0.21360.61760.37480.2008-0.0859-0.04920.43550.02680.293811.11630.378188.0822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:23)
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:46)
3X-RAY DIFFRACTION3chain 'A' and (resseq 47:59)
4X-RAY DIFFRACTION4chain 'A' and (resseq 60:82)
5X-RAY DIFFRACTION5chain 'A' and (resseq 83:108)

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