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- PDB-4gwo: Crystal structure of ligand binding domain of LysR family member,... -

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Basic information

Entry
Database: PDB / ID: 4gwo
TitleCrystal structure of ligand binding domain of LysR family member,CysB in complex with sulfate from Salmonella typhimurium LT2
ComponentsHTH-type transcriptional regulator CysB
KeywordsGENE REGULATION / LTTR / CysB / Sulfate / alpha/beta fold / Transcription regulation / N-acetyl serine binding / DNA binding
Function / homology
Function and homology information


L-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 TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsMittal, M. / Singh, A.K. / Kumaran, S.
CitationJournal: To be Published
Title: Crystal structure of ligand binding domain of LysR family member,CysB in complex with sulfate from Salmonella typhimurium LT2
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,0565
Polymers73,7722
Non-polymers2843
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-54 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.921, 105.301, 47.751
Angle α, β, γ (deg.)90.00, 103.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 87:91 OR RESSEQ 93:120 OR RESSEQ...
211CHAIN B AND (RESSEQ 87:91 OR RESSEQ 93:120 OR RESSEQ...

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Components

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


Mass: 36886.000 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP residues 86-324
Source method: isolated from a genetically manipulated source
Details: IPTG inducible / Source: (gene. exp.) SALMONELLA 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30%(w/v) PEG5000 MME,0.2M ammonium sulphate, 0.1M MES, pH 6.5, 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: Jun 18, 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: 2.394→45.71 Å / Num. all: 47731 / Num. obs: 17828 / % possible obs: 67.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 38.14

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AL3

1al3


Resolution: 2.394→26.325 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 1.36 / Phase error: 32.29 / Stereochemistry target values: ML
Details: DURING CRYSTALLIZATION, CYSB N-TERMINAL DOMAIN CLEAVED AND COULD NOT BE FOUND WHEN RUNNING IN THE GEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 822 5.09 %RANDOM
Rwork0.1984 ---
obs0.2019 16162 90.77 %-
all-47731 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.13 Å2
Refinement stepCycle: LAST / Resolution: 2.394→26.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 16 17 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013837
X-RAY DIFFRACTIONf_angle_d1.4045241
X-RAY DIFFRACTIONf_dihedral_angle_d16.6651352
X-RAY DIFFRACTIONf_chiral_restr0.113606
X-RAY DIFFRACTIONf_plane_restr0.006670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1811X-RAY DIFFRACTIONPOSITIONAL
12B1811X-RAY DIFFRACTIONPOSITIONAL0.095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.394-2.54410.3311050.2193187167
2.5441-2.74040.32431280.2408231582
2.7404-3.01580.33661310.248272697
3.0158-3.45140.30121500.23382808100
3.4514-4.34520.25881470.1921280999
4.3452-26.32680.22731610.1666281199

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