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- PDB-2y7w: DntR Inducer Binding Domain -

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Basic information

Entry
Database: PDB / ID: 2y7w
TitleDntR Inducer Binding Domain
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION
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
2-HYDROXYBENZOIC ACID / LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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 2, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,89310
Polymers103,8964
Non-polymers9976
Water95553
1
A: LYSR-TYPE REGULATORY PROTEIN
B: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8077
Polymers51,9482
Non-polymers8595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-15.2 kcal/mol
Surface area17990 Å2
MethodPISA
2
C: LYSR-TYPE REGULATORY PROTEIN
D: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0863
Polymers51,9482
Non-polymers1381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-20.5 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.187, 118.957, 80.558
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 92:133 OR RESSEQ 139:157 OR RESSEQ...
211CHAIN B AND (RESSEQ 92:133 OR RESSEQ 139:157 OR RESSEQ...
311CHAIN C AND (RESSEQ 92:133 OR RESSEQ 139:157 OR RESSEQ...
411CHAIN D AND (RESSEQ 92:133 OR RESSEQ 139:157 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(-0.98598, 0.00791, 0.1667), (-0.01276, -0.99952, -0.02808), (0.1664, -0.02981, 0.98561)52.87601, 33.13368, -4.02276
2given(0.8074, -0.00788, 0.58995), (-0.00902, -0.99996, -0.00101), (0.58994, -0.0045, -0.80744)-7.00677, 12.37242, 22.22477
3given(-0.67324, 0.0032, -0.73942), (-0.01141, 0.99983, 0.01472), (0.73934, 0.01835, -0.67308)64.33035, 20.14898, 14.99059

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Components

#1: Protein
LYSR-TYPE REGULATORY PROTEIN


Mass: 25974.059 Da / Num. of mol.: 4 / Fragment: INDUCER BINDING DOMAIN, RESIDUES 80-301 / 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
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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
Nonpolymer detailsPEG 400 (PG4): PEG 3350 IN CRYSTALLISATION CONDITIONS MODELLED AS PEG 400

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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 USED AS SEPARATE SEARCH MODELS
Crystal growDetails: 0.1M BIS-TRIS PH 6.5, 0.2M MGCL2, 25% PEG 3350

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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: 2.9→47.1 Å / Num. obs: 20475 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.4
Reflection shellResolution: 2.89→3.04 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.7 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.4_94)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTB, MOLECULE A

1utb


Resolution: 2.89→47.14 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 30.39 / Stereochemistry target values: ML
Details: FOR ALL CHAINS IN THE ASYMMETRIC UNIT ELECTRON DENSITY FOR AMINO ACIDS ALA 201 TO VAL 209 IS DISORDERED. THE MODEL IN THESE REGIONS SHOULD BE TREATED WITH CAUTION.
RfactorNum. reflection% reflection
Rfree0.287 1057 5.2 %
Rwork0.242 --
obs0.244 20450 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.22 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.2822 Å20 Å24.5373 Å2
2---5.3834 Å20 Å2
3---0.1011 Å2
Refinement stepCycle: LAST / Resolution: 2.89→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 69 53 6502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016625
X-RAY DIFFRACTIONf_angle_d1.4098995
X-RAY DIFFRACTIONf_dihedral_angle_d17.5822364
X-RAY DIFFRACTIONf_chiral_restr0.0871008
X-RAY DIFFRACTIONf_plane_restr0.0061158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1436X-RAY DIFFRACTIONPOSITIONAL
12B1436X-RAY DIFFRACTIONPOSITIONAL0.066
13C1446X-RAY DIFFRACTIONPOSITIONAL0.049
14D1421X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8854-3.01670.3681270.3082240X-RAY DIFFRACTION87
3.0167-3.17570.38691440.2952397X-RAY DIFFRACTION94
3.1757-3.37460.3311270.26872449X-RAY DIFFRACTION94
3.3746-3.63510.27471190.23662449X-RAY DIFFRACTION94
3.6351-4.00070.24981380.22252430X-RAY DIFFRACTION95
4.0007-4.57920.27391210.20812467X-RAY DIFFRACTION95
4.5792-5.76770.2311450.20412470X-RAY DIFFRACTION95
5.7677-47.14950.26171360.23092491X-RAY DIFFRACTION95

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