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- PDB-2y84: DntR Inducer Binding Domain -

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Basic information

Entry
Database: PDB / ID: 2y84
TitleDntR Inducer Binding Domain
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA SP. DNT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDevesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Crystal Structures of Dntr Inducer Binding Domains in Complex with Salicylate Offer Insights Into the Activation of Lysr-Type Transcriptional Regulators.
Authors: Devesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
History
DepositionFeb 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: LYSR-TYPE REGULATORY PROTEIN
B: LYSR-TYPE REGULATORY PROTEIN
C: LYSR-TYPE REGULATORY PROTEIN
D: LYSR-TYPE REGULATORY PROTEIN
E: LYSR-TYPE REGULATORY PROTEIN
F: LYSR-TYPE REGULATORY PROTEIN
G: LYSR-TYPE REGULATORY PROTEIN
H: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,16112
Polymers207,7928
Non-polymers3684
Water1,874104
1
A: LYSR-TYPE REGULATORY PROTEIN
E: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0403
Polymers51,9482
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26.9 kcal/mol
Surface area18540 Å2
MethodPISA
2
B: LYSR-TYPE REGULATORY PROTEIN
D: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1324
Polymers51,9482
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23.3 kcal/mol
Surface area18260 Å2
MethodPISA
3
C: LYSR-TYPE REGULATORY PROTEIN
H: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0403
Polymers51,9482
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-22.9 kcal/mol
Surface area18220 Å2
MethodPISA
4
F: LYSR-TYPE REGULATORY PROTEIN
G: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,9482
Polymers51,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23.2 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.200, 111.500, 213.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99629, -0.00188, -0.086), (0.08588, -0.03565, 0.99567), (-0.00494, -0.99936, -0.03536)-21.62824, 25.47991, 27.27436
2given(-0.99991, -0.00624, 0.01227), (0.00066, -0.91206, -0.41005), (0.01375, -0.41001, 0.91198)45.81065, 53.57639, 10.82479
3given(0.85241, 0.47309, 0.22265), (0.19666, 0.10447, -0.97489), (-0.48447, 0.8748, -0.00398)-10.9773, -34.5289, 33.31361
4given(0.8189, 0.2672, -0.50795), (0.27068, -0.96021, -0.06872), (-0.50611, -0.08121, -0.85864)13.64402, -1.93018, 48.64793
5given(-0.99412, -0.03594, 0.10211), (-0.10812, 0.37671, -0.92), (-0.0054, -0.92564, -0.37838)65.1322, 22.76765, 25.35604
6given(-0.85465, 0.51918, -0.00508), (-0.19107, -0.3054, 0.93286), (0.48276, 0.79824, 0.36021)61.51928, -6.62655, -6.53642
7given(-0.82411, -0.05311, -0.56393), (-0.2868, 0.89766, 0.33459), (0.48845, 0.43747, -0.755)60.52948, -41.12528, 11.47396

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Components

#1: Protein
LYSR-TYPE REGULATORY PROTEIN / DNTR


Mass: 25974.059 Da / Num. of mol.: 8 / Fragment: INDUCER-BINDING DOMAIN, RESIDUES 80-301 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA SP. DNT (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 80 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN E, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN F, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN G, LEU 80 TO MET ENGINEERED RESIDUE IN CHAIN H, LEU 80 TO MET
Sequence detailsPHE 80 WAS MUTATED TO INTRODUCE AN INITIATION METHIONINE

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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: 2.32 Å3/Da / Density % sol: 47 %
Description: RD1, RD2 DOMAINS USED AS SEPARATE SEARCH MODELS
Crystal growDetails: 0.2 M NA/K TARTRATE, 0.1 M TRIS PH 8.0, 33% PEG 8000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→49.5 Å / Num. obs: 47128 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTB

1utb


Resolution: 2.8→48.229 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 2436 5.1 %
Rwork0.2178 --
obs0.2191 48165 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.762 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.5823 Å20 Å20 Å2
2---5.0019 Å20 Å2
3---0.1253 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13422 0 24 104 13550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313875
X-RAY DIFFRACTIONf_angle_d0.7518831
X-RAY DIFFRACTIONf_dihedral_angle_d17.9775115
X-RAY DIFFRACTIONf_chiral_restr0.0522067
X-RAY DIFFRACTIONf_plane_restr0.0032458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.90010.3442320.31814282X-RAY DIFFRACTION95
2.9001-3.01620.3492570.29694482X-RAY DIFFRACTION99
3.0162-3.15350.30682370.27544532X-RAY DIFFRACTION100
3.1535-3.31970.27272450.23954543X-RAY DIFFRACTION100
3.3197-3.52760.27622480.21694590X-RAY DIFFRACTION100
3.5276-3.79990.2382310.19774556X-RAY DIFFRACTION100
3.7999-4.18210.19352540.17974605X-RAY DIFFRACTION100
4.1821-4.78680.1792360.16274629X-RAY DIFFRACTION100
4.7868-6.0290.20872580.18394657X-RAY DIFFRACTION100
6.029-48.2360.21032380.20184853X-RAY DIFFRACTION99

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