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- PDB-2y7r: DntR Inducer Binding Domain -

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Basic information

Entry
Database: PDB / ID: 2y7r
TitleDntR Inducer Binding Domain
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION REGULATOR / TRANSCRIPTION / LYSR TYPE TRANSCRIPTION FACTOR
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 ...: / 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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)198,7038
Polymers198,7038
Non-polymers00
Water00
1
D: LYSR-TYPE REGULATORY PROTEIN
H: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-27.4 kcal/mol
Surface area18430 Å2
MethodPISA
2
B: LYSR-TYPE REGULATORY PROTEIN
F: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-27.1 kcal/mol
Surface area18100 Å2
MethodPISA
3
C: LYSR-TYPE REGULATORY PROTEIN
G: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-25.9 kcal/mol
Surface area18310 Å2
MethodPISA
4
A: LYSR-TYPE REGULATORY PROTEIN
E: LYSR-TYPE REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)49,6762
Polymers49,6762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22.2 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.473, 125.003, 184.841
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(-0.99995, 0.00469, 0.00905), (0.00577, 0.99232, 0.1236), (-0.0084, 0.12365, -0.99229)1.9652, 0.12432, -3.47784
2given(-0.99834, -0.03353, 0.04688), (0.05052, -0.11753, 0.99178), (-0.02774, 0.9925, 0.11903)24.4923, 35.29449, -31.30251
3given(0.87558, 0.40568, -0.26226), (0.40668, -0.91203, -0.05307), (-0.26072, -0.06019, -0.96354)4.61094, -17.38171, 7.05825
4given(-0.8734, 0.36291, 0.32477), (-0.40616, -0.91076, -0.07456), (0.26873, -0.19703, 0.94285)7.09424, -16.50521, 9.92107
5given(-0.85007, -0.27382, 0.44988), (-0.48048, 0.05343, -0.87538), (0.21566, -0.96029, -0.17699)47.77568, -38.20033, 29.71514
6given(0.86453, 0.26231, 0.42871), (0.42396, 0.07747, -0.90236), (-0.26991, 0.96187, -0.04424)-6.60652, -57.13587, -18.43282

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Components

#1: Protein
LYSR-TYPE REGULATORY PROTEIN / DNTR


Mass: 24837.824 Da / Num. of mol.: 8 / Fragment: INDUCER BINDING DOMAIN, RESIDUES 90-301 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA SP. (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50

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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 AND RD2 USED AS SEPARATE SEARCH MODELS
Crystal growDetails: 0.2 M NA/K TARTRATE, 0.1 M TRIS PH 8.0-8.5; PEG 8000 28-30%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→44 Å / Num. obs: 37607 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTB, CHAIN A

1utb


Resolution: 2.99→43.9 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.843 / SU B: 19.915 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1883 5 %RANDOM
Rwork0.19364 ---
obs0.1972 35722 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.876 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.99→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12995 0 0 0 12995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213355
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.96118157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44322.458541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74152084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061592
X-RAY DIFFRACTIONr_chiral_restr0.10.22033
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02210176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.58474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.013213634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35934881
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3934.54523
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.987→3.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 142 -
Rwork0.272 2546 -
obs--96.38 %

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