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- PDB-4m4g: Crystal structure of ligand binding domain of CysB, a LysR member... -

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Basic information

Entry
Database: PDB / ID: 4m4g
TitleCrystal structure of ligand binding domain of CysB, a LysR member from Salmonella typhimurium LT2 in complex with effector ligand, N-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
DI(HYDROXYETHYL)ETHER / N-ACETYL-SERINE / HTH-type transcriptional regulator CysB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 LT2 in complex with effector ligand, N-acetylserine
Authors: Mittal, M. / Singh, A.K. / Kumaran, S.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)27,9194
Polymers27,5181
Non-polymers4003
Water1086
1
A: HTH-type transcriptional regulator CysB
hetero molecules

A: HTH-type transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8378
Polymers55,0362
Non-polymers8016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2760 Å2
ΔGint-4 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.736, 74.300, 104.732
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
11A-403-

PEG

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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: C-TERMINAL DOMAIN
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-SAC / N-ACETYL-SERINE


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Fragment: SAC / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: PEG / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30%(w/v) PEG8000, 0.1M Sodium cacodylate, 0.2M Sodium acetate trihydrate, 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 FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 24, 2013 / Details: MSC/Yale double focusing mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 30495 / Num. obs: 30495 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 22.67

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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 / Resolution: 2.7→26.183 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 299 4.66 %Random
Rwork0.2194 ---
obs0.2219 6422 99.35 %-
all-6422 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→26.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 27 6 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051902
X-RAY DIFFRACTIONf_angle_d0.8872597
X-RAY DIFFRACTIONf_dihedral_angle_d12.548659
X-RAY DIFFRACTIONf_chiral_restr0.051304
X-RAY DIFFRACTIONf_plane_restr0.004334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7-3.40010.35741500.25713003
3.4001-26.18420.24651490.20663120

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