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- PDB-4lq5: Crystal structure of ligand binding domain of CysB, a LysR member... -

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Basic information

Entry
Database: PDB / ID: 4lq5
TitleCrystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium LT2 in complex with effector ligand, O-acetylserine at 2.8A
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: 2.803 Å
AuthorsMittal, M. / Singh, A.K. / Kumaran, S.
CitationJournal: TO BE PUBLISHED
Title: rystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium LT2 in complex with effector ligand, O-acetylserine at 2.8A
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 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

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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)27,8123
Polymers27,5181
Non-polymers2942
Water21612
1
A: HTH-type transcriptional regulator CysB
hetero molecules

A: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6256
Polymers55,0362
Non-polymers5894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.979, 74.449, 103.576
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


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
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 18, 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: 2.8→50 Å / Num. all: 18561 / Num. obs: 18561 / % possible obs: 52.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.223 / Rsym value: 0.223 / Net I/σ(I): 18.634

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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: 2.803→41.845 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 218 4.29 %Random
Rwork0.2335 ---
obs0.2358 5077 88.14 %-
all-5077 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→41.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 20 12 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031895
X-RAY DIFFRACTIONf_angle_d0.6742589
X-RAY DIFFRACTIONf_dihedral_angle_d12.342661
X-RAY DIFFRACTIONf_chiral_restr0.049304
X-RAY DIFFRACTIONf_plane_restr0.002330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-3.53080.3445990.2703213879
3.5308-41.84920.261190.2198272197

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