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- PDB-5yix: Caulobacter crescentus GcrA sigma-interacting domain (SID) in com... -

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Basic information

Entry
Database: PDB / ID: 5yix
TitleCaulobacter crescentus GcrA sigma-interacting domain (SID) in complex with domain 2 of sigma 70
Components
  • Cell cycle regulatory protein GcrA
  • RNA polymerase sigma factor RpoD
KeywordsDNA BINDING PROTEIN / Caulobacter crescentus / GcrA / sigma-interacting domain / transcription factor
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
GcrA cell cycle regulator / GcrA cell cycle regulator / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. ...GcrA cell cycle regulator / GcrA cell cycle regulator / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Cell cycle regulatory protein GcrA / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å
AuthorsWu, X. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670067 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.
Authors: Wu, X. / Haakonsen, D.L. / Sanderlin, A.G. / Liu, Y.J. / Shen, L. / Zhuang, N. / Laub, M.T. / Zhang, Y.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RNA polymerase sigma factor RpoD
B: Cell cycle regulatory protein GcrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0695
Polymers49,8232
Non-polymers2463
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.199, 65.199, 397.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

#1: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 40153.219 Da / Num. of mol.: 1 / Fragment: domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: rpoD, CCNA_03142 / Details (production host): pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CAV3
#2: Protein Cell cycle regulatory protein GcrA


Mass: 9669.998 Da / Num. of mol.: 1 / Fragment: sigma-interacting domain (SID)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: NA1000 / CB15N / Gene: gcrA, CCNA_02328 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3C9J4
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H10O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 3350, 0.1M sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 295.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 23503 / % possible obs: 98.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03 / Rrim(I) all: 0.12 / Rsym value: 0.11 / Χ2: 1.04 / Net I/σ(I): 29.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2028 / CC1/2: 0.91 / Rpim(I) all: 0.2 / Rrim(I) all: 0.78 / Rsym value: 0.75 / Χ2: 0.95 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.302→40.061 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.87
RfactorNum. reflection% reflection
Rfree0.2565 1163 4.97 %
Rwork0.2221 --
obs0.224 23395 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.17 Å2
Refinement stepCycle: LAST / Resolution: 2.302→40.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 0 182 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082931
X-RAY DIFFRACTIONf_angle_d0.9473944
X-RAY DIFFRACTIONf_dihedral_angle_d14.9061080
X-RAY DIFFRACTIONf_chiral_restr0.034447
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3019-2.40660.35071320.28112529X-RAY DIFFRACTION93
2.4066-2.53350.28051290.26652715X-RAY DIFFRACTION100
2.5335-2.69220.31851480.25172737X-RAY DIFFRACTION100
2.6922-2.90.30331430.24452722X-RAY DIFFRACTION100
2.9-3.19170.29851320.24092791X-RAY DIFFRACTION100
3.1917-3.65330.22651590.21472799X-RAY DIFFRACTION100
3.6533-4.60170.21411450.18842860X-RAY DIFFRACTION100
4.6017-40.06710.24351750.20973079X-RAY DIFFRACTION100

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