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- PDB-4lq2: Crystal structure of ligand binding domain of CysB, a LysR member... -

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Basic information

Entry
Database: PDB / ID: 4lq2
TitleCrystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium in complex with effector ligand, O-acetylserine
ComponentsHTH-type transcriptional regulator CysB
KeywordsGENE REGULATION / wHTH motif/ PBP type II alpha/beta fold / Rossmann fold / LTTR / Transcriptional Regulation / O-acetyl serine / N-acetyl serine binding / DNA binding / Cytoplasmic
Function / homology
Function and homology information


cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
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
O-ACETYLSERINE / HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.694 Å
AuthorsMittal, M. / Singh, A.K. / Kumaran, S.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium in complex with effector ligand, O-acetylserine
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6652
Polymers27,5181
Non-polymers1471
Water23413
1
A: HTH-type transcriptional regulator CysB
hetero molecules

A: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3314
Polymers55,0362
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2420 Å2
ΔGint-14 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.496, 73.761, 104.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HTH-type transcriptional regulator CysB / Cys regulon transcriptional activator


Mass: 27518.223 Da / Num. of mol.: 1 / Fragment: UNP residues 86-324
Source method: isolated from a genetically manipulated source
Details: IPTG Inducible
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: cysB, STM1713 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P06614
#2: Chemical ChemComp-OAS / O-ACETYLSERINE / O-Acetylserine


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30%(w/v) PEG4000, 0.1M Tris pH 8.5, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 2013
RadiationMonochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 5882 / % possible obs: 65.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.306 / Rsym value: 0.306 / Net I/σ(I): 35.209

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AL3

1al3


Resolution: 2.694→45.347 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 268 4.58 %
Rwork0.2293 --
obs0.2322 5852 91.24 %
all-5852 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.349 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.712 Å20 Å2-0 Å2
2--17.3221 Å2-0 Å2
3----13.61 Å2
Refinement stepCycle: LAST / Resolution: 2.694→45.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 10 13 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091865
X-RAY DIFFRACTIONf_angle_d1.2492552
X-RAY DIFFRACTIONf_dihedral_angle_d16.62645
X-RAY DIFFRACTIONf_chiral_restr0.078300
X-RAY DIFFRACTIONf_plane_restr0.006329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6941-3.39410.4221220.27832558X-RAY DIFFRACTION85
3.3941-45.35330.25271460.2143026X-RAY DIFFRACTION97

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