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- PDB-5z7i: Caulobacter crescentus GcrA DNA-binding domain(DBD)in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5z7i
TitleCaulobacter crescentus GcrA DNA-binding domain(DBD)in complex with unmethylated dsDNA
Components
  • Cell cycle regulatory protein GcrA
  • DNA (5'-D(*CP*CP*CP*TP*GP*AP*TP*TP*CP*GP*C*)-3')
  • DNA (5'-D(P*GP*CP*GP*AP*AP*TP*CP*AP*GP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / Caulobacter crescentus / GcrA / DNA-binding / transcription factor / DNA binding protein / DNA BINDING PROTEIN-DNA complex
Function / homologyGcrA cell cycle regulator / GcrA cell cycle regulator / metal ion binding / (R,R)-2,3-BUTANEDIOL / DNA / DNA (> 10) / Cell cycle regulatory protein GcrA
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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
DepositionJan 29, 2018Deposition 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell cycle regulatory protein GcrA
B: Cell cycle regulatory protein GcrA
C: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*AP*TP*TP*CP*GP*C*)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4216
Polymers22,3315
Non-polymers901
Water3,117173
1
A: Cell cycle regulatory protein GcrA
D: DNA (5'-D(*CP*CP*CP*TP*GP*AP*TP*TP*CP*GP*C*)-3')
E: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7874
Polymers11,6963
Non-polymers901
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-17 kcal/mol
Surface area5770 Å2
MethodPISA
2
B: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2970 Å2
MethodPISA
3
C: Cell cycle regulatory protein GcrA


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.909, 64.896, 126.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide Cell cycle regulatory protein GcrA


Mass: 5317.199 Da / Num. of mol.: 3
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: plasmid / Details (production host): pRT28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3C9J4
#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*GP*AP*TP*TP*CP*GP*C*)-3')


Mass: 3285.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*GP*AP*AP*TP*CP*AP*GP*G)-3')


Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.05M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 27384 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.37 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rsym value: 0.08 / Net I/σ(I): 22.05
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.959 / Rpim(I) all: 0.38 / Rsym value: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IGV2

Resolution: 1.601→28.869 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1344 4.93 %
Rwork0.2001 --
obs0.2013 27251 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→28.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 426 6 173 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071522
X-RAY DIFFRACTIONf_angle_d0.9632149
X-RAY DIFFRACTIONf_dihedral_angle_d21.268574
X-RAY DIFFRACTIONf_chiral_restr0.038259
X-RAY DIFFRACTIONf_plane_restr0.006191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.65830.32081190.2812522X-RAY DIFFRACTION98
1.6583-1.72460.26921390.24832517X-RAY DIFFRACTION98
1.7246-1.80310.24691420.22392556X-RAY DIFFRACTION100
1.8031-1.89820.24751430.22882584X-RAY DIFFRACTION100
1.8982-2.01710.2491300.22362577X-RAY DIFFRACTION100
2.0171-2.17280.21271430.20682603X-RAY DIFFRACTION100
2.1728-2.39130.24641200.21442617X-RAY DIFFRACTION100
2.3913-2.73710.27671240.21772640X-RAY DIFFRACTION100
2.7371-3.44760.22671400.20422602X-RAY DIFFRACTION99
3.4476-28.8740.1911440.17312689X-RAY DIFFRACTION98

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