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- PDB-3lsj: Crystal structure of DesT in complex with palmitoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 3lsj
TitleCrystal structure of DesT in complex with palmitoyl-CoA
ComponentsDesT
KeywordsTRANSCRIPTION / Transcriptional Repressor / DesT / TetR family / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription repressor activity / negative regulation of fatty acid metabolic process / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
Similarity search - Function
Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COENZYME A / PALMITIC ACID / DesT
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiller, D.J. / White, S.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for the transcriptional regulation of membrane lipid homeostasis.
Authors: Miller, D.J. / Zhang, Y.M. / Subramanian, C. / Rock, C.O. / White, S.W.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DesT
B: DesT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0496
Polymers48,0012
Non-polymers2,0484
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-25 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.677, 100.466, 60.838
Angle α, β, γ (deg.)90.00, 105.15, 90.00
Int Tables number4
Space group name H-MP1211
Detailshomodimer in asymmetric unit

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Components

#1: Protein DesT


Mass: 24000.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: desT, PA4890 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9HUS3
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ML- 0.1M HEPES, pH 7.5, 0.1 M magnesium acetate, 15% PEG 4000. Drop- 20 mg/ml protein, 0.9 mM 16:0-CoA. 2+2 ul drop., VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 21188 / Num. obs: 21188 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 2.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.76 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.419 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 1087 5.1 %RANDOM
Rwork0.22282 ---
obs0.22551 20078 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.1 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 130 179 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213341
X-RAY DIFFRACTIONr_angle_refined_deg1.2192.014524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7555405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6522.028143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12415532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1791536
X-RAY DIFFRACTIONr_chiral_restr0.070.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212486
X-RAY DIFFRACTIONr_mcbond_it0.4841.52033
X-RAY DIFFRACTIONr_mcangle_it0.90823235
X-RAY DIFFRACTIONr_scbond_it1.33231308
X-RAY DIFFRACTIONr_scangle_it2.2494.51289
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 85 -
Rwork0.255 1495 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: -2.484 Å / Origin y: 19.291 Å / Origin z: -21.17 Å
111213212223313233
T0.0102 Å2-0.0186 Å20.0093 Å2-0.089 Å20.0029 Å2--0.0666 Å2
L0.63 °2-0.1702 °2-0.1147 °2-1.8029 °20.0912 °2--1.209 °2
S0.0418 Å °-0.0684 Å °0.0217 Å °-0.0183 Å °-0.0484 Å °0.0683 Å °-0.0365 Å °-0.0126 Å °0.0066 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 54
2X-RAY DIFFRACTION1A60 - 208
3X-RAY DIFFRACTION1B6 - 54
4X-RAY DIFFRACTION1B60 - 208
5X-RAY DIFFRACTION1C1
6X-RAY DIFFRACTION1D2

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