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- PDB-6cg8: Structure of C. crescentus GapR-DNA -

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Basic information

Entry
Database: PDB / ID: 6cg8
TitleStructure of C. crescentus GapR-DNA
Components
  • DNA (5'-D(*TP*TP*AP*AP*AP*AP*TP*TP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*AP*TP*TP*TP*TP*AP*A)-3')
  • UPF0335 protein B7Z12_12435
KeywordsDNA BINDING PROTEIN/DNA / GapR / DNA binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyGapR-like / GapR-like, DNA-binding domain / GapR-like, DNA-binding domain / DNA binding / DNA / DNA (> 10) / UPF0335 protein B7Z12_12435 / UPF0335 protein CCNA_03428
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.299 Å
AuthorsSchumacher, M.A.
CitationJournal: Cell / Year: 2018
Title: A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication.
Authors: Guo, M.S. / Haakonsen, D.L. / Zeng, W. / Schumacher, M.A. / Laub, M.T.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: UPF0335 protein B7Z12_12435
B: UPF0335 protein B7Z12_12435
D: UPF0335 protein B7Z12_12435
E: UPF0335 protein B7Z12_12435
C: DNA (5'-D(*TP*TP*AP*AP*AP*AP*TP*TP*AP*AP*A)-3')
F: DNA (5'-D(*TP*TP*TP*AP*AP*TP*TP*TP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)42,6756
Polymers42,6756
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-113 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.913, 35.579, 115.559
Angle α, β, γ (deg.)90.000, 90.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-104-

HOH

21E-127-

HOH

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Components

#1: Protein
UPF0335 protein B7Z12_12435


Mass: 8993.409 Da / Num. of mol.: 4 / Fragment: residues 13-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: B7Z12_12435, CA606_13135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A258D3B4, UniProt: B8H4R9*PLUS
#2: DNA chain DNA (5'-D(*TP*TP*AP*AP*AP*AP*TP*TP*AP*AP*A)-3')


Mass: 3364.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*AP*TP*TP*TP*TP*AP*A)-3')


Mass: 3337.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 400, CaCl2, HEPES

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.299→57.8 Å / Num. obs: 32492 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rpim(I) all: 0.071 / Rsym value: 0.079 / Net I/σ(I): 7.6
Reflection shellResolution: 2.299→2.34 Å / Redundancy: 3.5 % / Num. unique obs: 3035 / CC1/2: 0.956 / Rpim(I) all: 0.267 / Rsym value: 0.358 / % possible all: 98

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.299→57.779 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2771 2419 7.44 %
Rwork0.249 --
obs0.251 32492 95.59 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 59.91 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 197.7 Å2 / Biso mean: 57.27 Å2 / Biso min: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1--9.0362 Å20 Å2-0.6789 Å2
2--16.9343 Å20 Å2
3----7.8981 Å2
Refinement stepCycle: final / Resolution: 2.299→57.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 445 0 103 3010
Biso mean---44.88 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022980
X-RAY DIFFRACTIONf_angle_d0.694072
X-RAY DIFFRACTIONf_chiral_restr0.035460
X-RAY DIFFRACTIONf_plane_restr0.001457
X-RAY DIFFRACTIONf_dihedral_angle_d18.8751219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.299-2.38120.27082400.23493056329695
2.3812-2.47650.29112330.2532801303491
2.4765-2.58930.35062360.25212943317994
2.5893-2.72580.2892400.25683118335897
2.7258-2.89650.29542430.25233063330698
2.8965-3.12020.27522480.27292983323196
3.1202-3.43410.32672360.28922980321694
3.4341-3.9310.26082500.23823133338398
3.931-4.95220.24172370.21272923316094
4.9522-57.79740.26592560.2573073332997
Refinement TLS params.Method: refined / Origin x: -5.9818 Å / Origin y: 6.3674 Å / Origin z: 28.8691 Å
111213212223313233
T0.1741 Å20.0077 Å20.0011 Å2-0.1581 Å2-0.0121 Å2--0.1771 Å2
L0.2302 °20.0938 °20.2132 °2-0.1494 °20.0674 °2--0.2685 °2
S-0.0678 Å °0.0137 Å °-0.007 Å °0.0119 Å °0.0013 Å °-0.0042 Å °0.0057 Å °-0.0387 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 88
2X-RAY DIFFRACTION1allB12 - 88
3X-RAY DIFFRACTION1allD12 - 88
4X-RAY DIFFRACTION1allE12 - 89
5X-RAY DIFFRACTION1allC3 - 13
6X-RAY DIFFRACTION1allF7 - 17
7X-RAY DIFFRACTION1allS1 - 104

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