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- PDB-7yhj: Effector binding domain of LysR-Type transcription factor LrhA fr... -

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Basic information

Entry
Database: PDB / ID: 7yhj
TitleEffector binding domain of LysR-Type transcription factor LrhA from E. coli
ComponentsProbable HTH-type transcriptional regulator LrhA
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Probable HTH-type transcriptional regulator LrhA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.237 Å
AuthorsXie, C. / Jiang, X.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Effector binding domain of LysR-Type transcription factor LrhA from E. coli
Authors: Xie, C. / Jiang, X.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable HTH-type transcriptional regulator LrhA
B: Probable HTH-type transcriptional regulator LrhA
C: Probable HTH-type transcriptional regulator LrhA
D: Probable HTH-type transcriptional regulator LrhA
E: Probable HTH-type transcriptional regulator LrhA
F: Probable HTH-type transcriptional regulator LrhA
G: Probable HTH-type transcriptional regulator LrhA
H: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,99311
Polymers284,6948
Non-polymers2983
Water39622
1
A: Probable HTH-type transcriptional regulator LrhA
C: Probable HTH-type transcriptional regulator LrhA
E: Probable HTH-type transcriptional regulator LrhA
G: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5496
Polymers142,3474
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-47 kcal/mol
Surface area31390 Å2
MethodPISA
2
B: Probable HTH-type transcriptional regulator LrhA
H: Probable HTH-type transcriptional regulator LrhA

D: Probable HTH-type transcriptional regulator LrhA
F: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4435
Polymers142,3474
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area6830 Å2
ΔGint-53 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.682, 169.312, 190.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable HTH-type transcriptional regulator LrhA


Mass: 35586.805 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lrhA, genR, b2289, JW2284 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P36771
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.81 % / Description: plate crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, 0.1 M HEPES, 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 43674 / % possible obs: 98.5 % / Redundancy: 5.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.172 / Rrim(I) all: 0.462 / Net I/σ(I): 3.2
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.385 / Num. unique obs: 4278 / CC1/2: 0.5 / Rpim(I) all: 0.89 / Rrim(I) all: 2.385 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONM

3onm


Resolution: 3.237→48.713 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3376 2148 4.94 %RANDOM
Rwork0.3208 41343 --
obs0.3217 43491 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.45 Å2 / Biso mean: 36.6604 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 3.237→48.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11809 0 17 22 11848
Biso mean--52.27 30 -
Num. residues----1532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.237-3.3120.40051460.3466240788
3.312-3.39480.32881410.3449270896
3.3948-3.48660.35421380.3435269698
3.4866-3.58910.371150.3341276298
3.5891-3.70490.38581400.3265272298
3.7049-3.83730.33661660.3108272098
3.8373-3.99090.34131450.3091274698
3.9909-4.17240.31441270.3109275298
4.1724-4.39220.33421440.2964276298
4.3922-4.66720.31421550.3009275798
4.6672-5.02720.31421490.3278098
5.0272-5.53250.33311240.3128283299
5.5325-6.33160.3271640.3164281099
6.3316-7.97150.35311560.3268287399
7.9715-48.7130.32631380.3502301699

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