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- PDB-2uyf: Single mutant F111L DntR from Burkholderia sp. strain DNT in comp... -

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Basic information

Entry
Database: PDB / ID: 2uyf
TitleSingle mutant F111L 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
ACETATE ION / 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 1.3Dec 13, 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: REGULATORY PROTEIN
B: REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,48719
Polymers69,3622
Non-polymers1,12417
Water3,747208
1
A: REGULATORY PROTEIN
B: REGULATORY PROTEIN
hetero molecules

A: REGULATORY PROTEIN
B: REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,97338
Polymers138,7244
Non-polymers2,24934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area7410 Å2
ΔGint-23.3 kcal/mol
Surface area44650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)106.604, 106.604, 296.448
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.53179, -0.82093, 0.20804), (-0.82305, 0.44312, -0.3553), (0.19949, -0.36017, -0.91131)
Vector: 100.34456, 90.02476, 132.36646)

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Components

#1: Protein REGULATORY PROTEIN / DNTR


Mass: 34681.074 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: STRAIN DNT / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/PREP4 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 111 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 111 TO LEU

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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: 4.67 Å3/Da / Density % sol: 73.44 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M IMIDAZOL PH 6.5 0.2M KSCN 1.2M 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→30 Å / Num. obs: 51204 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Biso Wilson estimate: 39.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
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→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.843 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A88 AND B1-B75 ARE DISORDERED. ATOMS BGLN A 292 CG (78.479, 7.234, 105.723, 32.55), CD (77.505, 7.365, 106.893, 34.27), OE1 (77. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-A88 AND B1-B75 ARE DISORDERED. ATOMS BGLN A 292 CG (78.479, 7.234, 105.723, 32.55), CD (77.505, 7.365, 106.893, 34.27), OE1 (77.015, 6.365, 107.423, 32.48), NE2 (77.234, 8.597, 107.299, 33.25) HAVE 0.00 OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2641 5.2 %RANDOM
Rwork0.207 ---
obs0.208 48457 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 64 208 3713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.974836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86422.194155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16815573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2711532
X-RAY DIFFRACTIONr_chiral_restr0.1290.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022714
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2730.21748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22412
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4420.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9191.52238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70723571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48131346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8794.51264
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
Rfree0.311 196
Rwork0.27 3243

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