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- PDB-4gxa: Crystal structure of Sulfate free form of CYSB, a member of LysR ... -

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Basic information

Entry
Database: PDB / ID: 4gxa
TitleCrystal structure of Sulfate free form of CYSB, a member of LysR family from Salmonella typhimurium LT2
ComponentsHTH-type transcriptional regulator CysB
KeywordsGENE REGULATION / LysR / CysB / Transcription / alpha/beta fold / Transcription regulation / 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
HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.807 Å
AuthorsMittal, M. / Singh, A.K. / Kumaran, S.
CitationJournal: To be Published
Title: Crystal structure of Sulfate free form of CYSB, a member of LysR family from Salmonella typhimurium LT2
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: 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
A: HTH-type transcriptional regulator CysB
B: HTH-type transcriptional regulator CysB


Theoretical massNumber of molelcules
Total (without water)53,3792
Polymers53,3792
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-10 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.484, 104.830, 46.505
Angle α, β, γ (deg.)90.00, 102.67, 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 86:120 OR RESSEQ 122:135 OR RESSEQ 137:151 OR RESSEQ 157:324 )
211CHAIN B AND (RESSEQ 86:120 OR RESSEQ 122:135 OR RESSEQ 137:151 OR RESSEQ 157:324 )

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Components

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


Mass: 26689.342 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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / Gene: cysB, STM1713 / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3 / References: UniProt: P06614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) PEG 8K, 0.2M magnesium acetate, 0.1M sodium cacodylate, 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: Aug 10, 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: 2.8→50 Å / Num. obs: 9669 / % possible obs: 90.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 28

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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: 2.807→45.372 Å / SU ML: 0.33 / Isotropic thermal model: isotropic / σ(F): 1.35 / Phase error: 32.39 / 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
Rfree0.2572 458 4.75 %RANDOM
Rwork0.1944 ---
obs0.1974 9642 90.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.6 Å2
Refinement stepCycle: LAST / Resolution: 2.807→45.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 0 10 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013724
X-RAY DIFFRACTIONf_angle_d1.5465095
X-RAY DIFFRACTIONf_dihedral_angle_d17.7481293
X-RAY DIFFRACTIONf_chiral_restr0.134601
X-RAY DIFFRACTIONf_plane_restr0.007651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1749X-RAY DIFFRACTIONPOSITIONAL
12B1749X-RAY DIFFRACTIONPOSITIONAL0.053
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 (%)
2.807-2.90.28721230.2089243572
3.2134-4.04820.29081850.2044331899
4.0482-45.37780.22641500.18593431100

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