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- PDB-2uye: Double mutant Y110S,F111V DntR from Burkholderia sp. strain DNT i... -

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Basic information

Entry
Database: PDB / ID: 2uye
TitleDouble mutant Y110S,F111V DntR from Burkholderia sp. strain DNT in complex with thiocyanate
ComponentsREGULATORY PROTEIN
KeywordsTRANSCRIPTION / LTTR / LYSR / DNA-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTIONAL REGULATOR
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
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
THIOCYANATE ION / Putative regulatory protein
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLonneborg, R. / Smirova, I. / Dian, C. / leonard, G.A. / McSweeney, S. / Brzezinski, P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: In Vivo and in Vitro Investigation of Transcriptional Regulation by Dntr.
Authors: Lonneborg, R. / Smirova, I. / Dian, C. / Leonard, G.A. / Brzezinski, P.
History
DepositionApr 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 4, 2020Group: Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: REGULATORY PROTEIN
B: REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15517
Polymers69,1822
Non-polymers97315
Water3,945219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-69 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.874, 106.874, 296.888
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.52347, -0.82519, 0.21222), (-0.82719, 0.43246, -0.35879), (0.20429, -0.36336, -0.90897)
Vector: 99.35409, 90.53486, 131.76492)

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Components

#1: Protein REGULATORY PROTEIN / DNTR


Mass: 34590.949 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: DNT / Plasmid: PQE60 / Cell line (production host): M15/PREP4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8VUD7
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 110 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 111 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, TYR 110 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 111 TO VAL ENGINEERED RESIDUE IN CHAIN B, TYR 110 TO SER ENGINEERED RESIDUE IN CHAIN B, PHE 111 TO VAL

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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: 4.7 Å3/Da / Density % sol: 73.61 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M IMIDAZOL PH 6.5 0.2M KSCN 0.9M NA ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→67.57 Å / Num. obs: 50378 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Biso Wilson estimate: 43.38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
XDSdata reduction
XDSdata scaling
REFMAC- RIGID BODY REFINEMENT USING DATA IN RESOLUTION RANGE 30.0 - 3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTH

1uth


Resolution: 2.2→67.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.072 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A87, B1-B75 AND B135 ARE DISORDERED. ATOMS BARG A 168 CZ (94.774, 6.083, 89.947, 56.8), NH1 (95.971, 6.608, 90.140, 57.53), NH2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A87, B1-B75 AND B135 ARE DISORDERED. ATOMS BARG A 168 CZ (94.774, 6.083, 89.947, 56.8), NH1 (95.971, 6.608, 90.140, 57.53), NH2 (94.651, 4.778, 89.771, 57.73) HAVE 0.00 OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2582 5.1 %RANDOM
Rwork0.207 ---
obs0.208 47796 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.45 Å20 Å2
2--0.89 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 54 219 3687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9684818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7922.468154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57615587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3051531
X-RAY DIFFRACTIONr_chiral_restr0.1110.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022687
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2970.21785
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22392
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.52231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67323575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28831341
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5794.51242
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 175
Rwork0.282 3243

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