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- PDB-5i44: Structure of RacA-DNA complex; P21 form -

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Basic information

Entry
Database: PDB / ID: 5i44
TitleStructure of RacA-DNA complex; P21 form
Components
  • Chromosome-anchoring protein RacA
  • DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA / RacA / B. subtilis / axial filament / sporulation / DNA segregation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


asymmetric cell division / chromosome condensation / sporulation resulting in formation of a cellular spore / chromosome segregation / double-stranded DNA binding / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Chromosome-anchoring protein RacA / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR HTH family regulatory protein / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromosome-anchoring protein RacA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.621 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein.
Authors: Schumacher, M.A. / Lee, J. / Zeng, W.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Chromosome-anchoring protein RacA
A: Chromosome-anchoring protein RacA
D: Chromosome-anchoring protein RacA
E: Chromosome-anchoring protein RacA
G: Chromosome-anchoring protein RacA
F: Chromosome-anchoring protein RacA
H: Chromosome-anchoring protein RacA
I: Chromosome-anchoring protein RacA
J: Chromosome-anchoring protein RacA
K: Chromosome-anchoring protein RacA
U: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
T: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
Z: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
R: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
P: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
W: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)102,40816
Polymers102,40816
Non-polymers00
Water3,027168
1
B: Chromosome-anchoring protein RacA
A: Chromosome-anchoring protein RacA
D: Chromosome-anchoring protein RacA
E: Chromosome-anchoring protein RacA
U: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
W: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)39,2516
Polymers39,2516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-34 kcal/mol
Surface area18210 Å2
2
G: Chromosome-anchoring protein RacA
F: Chromosome-anchoring protein RacA
I: Chromosome-anchoring protein RacA
R: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
P: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)31,5795
Polymers31,5795
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-25 kcal/mol
Surface area14990 Å2
3
H: Chromosome-anchoring protein RacA
J: Chromosome-anchoring protein RacA
K: Chromosome-anchoring protein RacA
T: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
Z: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)31,5795
Polymers31,5795
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-24 kcal/mol
Surface area14970 Å2
4
B: Chromosome-anchoring protein RacA
A: Chromosome-anchoring protein RacA
D: Chromosome-anchoring protein RacA
E: Chromosome-anchoring protein RacA
U: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
W: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')

G: Chromosome-anchoring protein RacA
F: Chromosome-anchoring protein RacA
I: Chromosome-anchoring protein RacA
R: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
P: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')

H: Chromosome-anchoring protein RacA
J: Chromosome-anchoring protein RacA
K: Chromosome-anchoring protein RacA
T: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
Z: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)102,40816
Polymers102,40816
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
Buried area19290 Å2
ΔGint-89 kcal/mol
Surface area46440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.600, 68.500, 117.400
Angle α, β, γ (deg.)90.000, 97.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chromosome-anchoring protein RacA


Mass: 7671.763 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: racA, ywkC, BSU37030 / Production host: Escherichia coli (E. coli) / References: UniProt: P45870
#2: DNA chain
DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Mass: 4281.779 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, 0.1 M Tris 8.0, lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.62→500 Å / Num. obs: 49675 / % possible obs: 98.6 % / Redundancy: 5 % / Net I/σ(I): 15.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.621→500 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2688 3297 6.3 %
Rwork0.2391 --
obs-49675 94.6 %
Solvent computationBsol: 42.4305 Å2
Displacement parametersBiso max: 126.21 Å2 / Biso mean: 68.5164 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å219.126 Å2
2--13.228 Å20 Å2
3----12.919 Å2
Refinement stepCycle: final / Resolution: 2.621→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 1704 168 0 7088
Biso mean--51.17 --
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.234
X-RAY DIFFRACTIONc_mcbond_it3.2151.5
X-RAY DIFFRACTIONc_scbond_it5.2492
X-RAY DIFFRACTIONc_mcangle_it5.0912
X-RAY DIFFRACTIONc_scangle_it7.2392.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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