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- PDB-5yiu: Caulobacter crescentus GcrA DNA-binding domain (DBD) -

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Basic information

Entry
Database: PDB / ID: 5yiu
TitleCaulobacter crescentus GcrA DNA-binding domain (DBD)
ComponentsCell cycle regulatory protein GcrA
KeywordsDNA BINDING PROTEIN / Caulobacter crescentus / GcrA / DNA-binding / transcription factor
Function / homologyGcrA cell cycle regulator / GcrA cell cycle regulator / metal ion binding / Cell cycle regulatory protein GcrA
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 1.2Nov 22, 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: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.410, 37.100, 40.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Cell cycle regulatory protein GcrA


Mass: 5317.199 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (DBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain NA1000 / CB15N) (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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.4M sodium citrate, 1M HEPES sodium, pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 9567 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 10.25 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Rsym value: 0.08 / Χ2: 1.01 / Net I/σ(I): 20.9
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 14.9 / Num. unique obs: 467 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Rsym value: 0.12 / Χ2: 0.97 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GV2

1gv2


Resolution: 1.42→27.449 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 21.13
RfactorNum. reflection% reflection
Rfree0.2114 472 5.16 %
Rwork0.1832 --
obs0.1846 9146 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.3 Å2
Refinement stepCycle: LAST / Resolution: 1.42→27.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms371 0 0 50 421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005398
X-RAY DIFFRACTIONf_angle_d0.908542
X-RAY DIFFRACTIONf_dihedral_angle_d11.181156
X-RAY DIFFRACTIONf_chiral_restr0.05164
X-RAY DIFFRACTIONf_plane_restr0.00366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4201-1.62560.17991530.15492835X-RAY DIFFRACTION100
1.6256-2.0480.22251610.19192854X-RAY DIFFRACTION100
2.048-27.45380.2151580.18682985X-RAY DIFFRACTION100

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