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- PDB-2y7k: DntR Inducer Binding Domain in Complex with Salicylate. Monoclini... -

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Basic information

Entry
Database: PDB / ID: 2y7k
TitleDntR Inducer Binding Domain in Complex with Salicylate. Monoclinic crystal form
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / LYSR TYPE / TRANSCRIPTION REGULATOR
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
2-HYDROXYBENZOIC ACID / LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA SP. DNT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,23610
Polymers99,4074
Non-polymers8296
Water5,314295
1
A: LYSR-TYPE REGULATORY PROTEIN
B: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2566
Polymers49,7042
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-16.5 kcal/mol
Surface area18310 Å2
MethodPISA
2
C: LYSR-TYPE REGULATORY PROTEIN
D: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9804
Polymers49,7042
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-17.5 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.905, 82.106, 86.273
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99849, -0.02999, 0.04611), (0.03806, -0.98193, 0.18538), (0.03972, 0.18686, 0.98158)31.53497, 5.61408, -0.71116
2given(0.17497, -0.05066, -0.98327), (-0.65401, -0.75249, -0.07761), (-0.73597, 0.65665, -0.16479)56.13278, 6.56766, 80.43185
3given(-0.10779, 0.00859, 0.99414), (0.47279, 0.88009, 0.04366), (-0.87456, 0.47473, -0.09893)-22.54134, 14.53691, 76.33982

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Components

#1: Protein
LYSR-TYPE REGULATORY PROTEIN / DNTR


Mass: 24851.852 Da / Num. of mol.: 4 / Fragment: INDUCER-BINDING DOMAIN, RESIDUES 90-301 / 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-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 90 TO MET ENGINEERED RESIDUE IN CHAIN B, PHE 90 TO MET ...ENGINEERED RESIDUE IN CHAIN A, PHE 90 TO MET ENGINEERED RESIDUE IN CHAIN B, PHE 90 TO MET ENGINEERED RESIDUE IN CHAIN C, PHE 90 TO MET ENGINEERED RESIDUE IN CHAIN D, PHE 90 TO MET
Sequence detailsSEQUENCE CRYSTALLIZED CONTAINS RESIDUES 90 - 301 OF Q7WT50 MUTATION F90M FOR EXPRESSION.

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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: NONE
Crystal growDetails: 31% PEG 8000, 0.1 M TRIS HCL PH 8.0, AND 0.2 M NA/K TARTRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→82.1 Å / Num. obs: 65440 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.265 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25002 3147 5.1 %RANDOM
Rwork0.19997 ---
obs0.20252 58885 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.249 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20.46 Å2
2---1.31 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 60 295 6971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.979356
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7222.241299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0971560
X-RAY DIFFRACTIONr_chiral_restr0.1120.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215308
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_it0.9481.54251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67726864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.59632632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0364.52486
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 223 -
Rwork0.262 4348 -
obs--99.13 %

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