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- PDB-8hig: Co-crystal structure of C-terminal DNA binding domain of Saccharo... -

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Basic information

Entry
Database: PDB / ID: 8hig
TitleCo-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA
Components
  • DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')
  • DNA-binding response OmpR family regulator
KeywordsTRANSCRIPTION/DNA / Transcription factor / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


phosphorelay signal transduction system / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding response OmpR family regulator
Similarity search - Component
Biological speciesSaccharopolyspora erythraea NRRL 2338 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å
AuthorsLin, W. / Xu, J.C. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: To Be Published
Title: Co-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA
Authors: Lin, W. / Xu, J.C. / Zhang, Y.
History
DepositionNov 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response OmpR family regulator
B: DNA-binding response OmpR family regulator
D: DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')
C: DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)67,5254
Polymers67,5254
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-29 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.279, 46.279, 366.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-108-

HOH

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Components

#1: Protein DNA-binding response OmpR family regulator / Transcriptional regulator


Mass: 27628.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
Strain: NRRL 2338 / Gene: glnR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4FQD5
#2: DNA chain DNA (5'-D(*AP*CP*GP*TP*AP*AP*CP*AP*TP*CP*GP*CP*GP*GP*TP*AP*AP*CP*AP*C)-3')


Mass: 6111.983 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
#3: DNA chain DNA (5'-D(*GP*TP*GP*TP*TP*AP*CP*CP*GP*CP*GP*AP*TP*GP*TP*TP*AP*CP*GP*T)-3')


Mass: 6155.975 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharopolyspora erythraea NRRL 2338 (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.68 Å3/Da / Density % sol: 26.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Bis-Tris pH5.7, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.329→50 Å / Num. obs: 19059 / % possible obs: 90.7 % / Redundancy: 5.1 % / CC1/2: 0.9 / Net I/σ(I): 11.146
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 2.034 / Num. unique obs: 569 / CC1/2: 0.107 / Rsym value: 1.62 / % possible all: 78.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.329→39.842 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3247 1325 9.98 %
Rwork0.2586 11948 -
obs0.2654 13273 63.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.48 Å2 / Biso mean: 23.4535 Å2 / Biso min: 1.45 Å2
Refinement stepCycle: final / Resolution: 2.329→39.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 812 0 48 2353
Biso mean---17.61 -
Num. residues----228
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3295-2.42270.4417610.36656928
2.4227-2.5330.4601740.365266533
2.533-2.66650.3779870.377982040
2.6665-2.83350.41761120.376199549
2.8335-3.05220.44071510.3483134065
3.0522-3.35920.33561890.2776164880
3.3592-3.8450.32771900.2419173482
3.845-4.84290.30272110.2095188490
4.8429-39.8420.24382500.2097229399

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