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

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Basic information

Entry
Database: PDB / ID: 5yiv
TitleCaulobacter crescentus GcrA DNA-binding domain(DBD) in complex with methylated dsDNA(crystal form 1)
Components
  • Cell cycle regulatory protein GcrA
  • DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')
  • DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / Caulobacter crescentus / GcrA / DNA-binding domain / transcription factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyGcrA cell cycle regulator / GcrA cell cycle regulator / metal ion binding / DNA / Cell cycle regulatory protein GcrA
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.914 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Cell cycle regulatory protein GcrA
E: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
F: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')
G: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
H: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')
I: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
J: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')
K: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
L: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)43,10712
Polymers43,10712
Non-polymers00
Water362
1
A: Cell cycle regulatory protein GcrA
E: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
F: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,7773
Polymers10,7773
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint1 kcal/mol
Surface area4960 Å2
MethodPISA
2
B: Cell cycle regulatory protein GcrA
G: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
H: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,7773
Polymers10,7773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint1 kcal/mol
Surface area4600 Å2
MethodPISA
3
C: Cell cycle regulatory protein GcrA
I: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
J: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,7773
Polymers10,7773
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint0 kcal/mol
Surface area5140 Å2
MethodPISA
4
D: Cell cycle regulatory protein GcrA
K: DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')
L: DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,7773
Polymers10,7773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint0 kcal/mol
Surface area4680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.017, 131.704, 77.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein/peptide
Cell cycle regulatory protein GcrA


Mass: 5317.199 Da / Num. of mol.: 4 / 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: DNA chain
DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')


Mass: 2720.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')


Mass: 2738.839 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.68 Å3/Da / Density % sol: 66.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8000, 0.1M Sodium cacodylate, pH 6.5, 0.2M Ammonium surface

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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: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13413 / % possible obs: 94.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 59.55 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.05 / Rrim(I) all: 0.12 / Rsym value: 0.11 / Χ2: 0.86 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→2.95 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1010 / CC1/2: 0.5 / Χ2: 0.71 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIU

5yiu


Resolution: 2.914→39.03 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2421 603 5.31 %
Rwork0.2006 --
obs0.2028 11348 79.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.47 Å2
Refinement stepCycle: LAST / Resolution: 2.914→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 1416 0 2 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042984
X-RAY DIFFRACTIONf_angle_d0.7284308
X-RAY DIFFRACTIONf_dihedral_angle_d26.5781144
X-RAY DIFFRACTIONf_chiral_restr0.03493
X-RAY DIFFRACTIONf_plane_restr0.002296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9139-3.2070.36651020.29631671X-RAY DIFFRACTION51
3.207-3.67080.27971370.22612684X-RAY DIFFRACTION80
3.6708-4.62360.24561840.20963188X-RAY DIFFRACTION95
4.6236-39.0330.20491800.16773202X-RAY DIFFRACTION92

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