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- PDB-4lp2: Crystal structure of monomeric ligand binding domain of S. typhim... -

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Basic information

Entry
Database: PDB / ID: 4lp2
TitleCrystal structure of monomeric ligand binding domain of S. typhimurium CysB, a LysR transcriptional regulator at 2.2A
ComponentsHTH-type transcriptional regulator CysB
KeywordsGENE REGULATION / LTTR / CysB / wHTH motif / alpha/beta fold / Rossmann fold / Transcription regulation / O-acetyl serine / N-acetyl serine binding / DNA binding
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
HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMittal, M. / Singh, A.K. / Kumaran, S.
CitationJournal: To be Published
Title: Crystal structure of monomeric ligand binding domain of S. typhimurium CysB, a LysR transcriptional regulator at 2.2A
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HTH-type transcriptional regulator CysB


Theoretical massNumber of molelcules
Total (without water)26,6891
Polymers26,6891
Non-polymers00
Water66737
1
B: HTH-type transcriptional regulator CysB

B: HTH-type transcriptional regulator CysB


Theoretical massNumber of molelcules
Total (without water)53,3792
Polymers53,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2460 Å2
ΔGint-9 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.808, 70.052, 105.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-403-

HOH

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Components

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


Mass: 26689.342 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M imidazole pH 6.5, 1.0M Sodium acetate, 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: Jul 14, 2011
RadiationMonochromator: Graphite polar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 30862 / Num. obs: 30862 / % possible obs: 78.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.178 / Rsym value: 0.178 / Net I/σ(I): 32.974

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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: 2.3→26.427 Å / SU ML: 0.3 / Isotropic thermal model: isotrpic / σ(F): 0 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 452 4.86 %random
Rwork0.2295 ---
obs0.2315 9303 94.02 %-
all-9303 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→26.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 0 37 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041915
X-RAY DIFFRACTIONf_angle_d0.9952613
X-RAY DIFFRACTIONf_dihedral_angle_d14.263682
X-RAY DIFFRACTIONf_chiral_restr0.065301
X-RAY DIFFRACTIONf_plane_restr0.003336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.62910.35541480.2944277390
2.6291-3.31130.36051780.2688306199
3.3113-26.42870.20761260.2021301793

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