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- PDB-2z3x: Structure of a Protein-DNA Complex Essential for DNA Protection i... -

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Basic information

Entry
Database: PDB / ID: 2z3x
TitleStructure of a Protein-DNA Complex Essential for DNA Protection in Spore of Bacillus Species
Components
  • 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*A)-3'
  • 5'-D(*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*A)-3'
  • Small, acid-soluble spore protein C
KeywordsDNA BINDING PROTEIN/DNA / alpha/beta-type SASP / Bacillus subtils spore / Protein-DNA complex / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / DNA topological change / double-stranded DNA binding
Similarity search - Function
Small, acid-soluble spore protein, alpha/beta type-like / Small acid-soluble spore protein, alpha/beta-type / SASP, alpha/beta-type superfamily / Small, acid-soluble spore proteins, alpha/beta type / Small, acid-soluble spore proteins, alpha/beta type, signature 1. / Small, acid-soluble spore proteins, alpha/beta type, signature 2. / Small acid-soluble spore protein, alpha/beta-type, conserved site / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special
Similarity search - Domain/homology
DNA / DNA (> 10) / Small, acid-soluble spore protein C
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLee, K.S. / Jedrzejas, M.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2008
Title: Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species.
Authors: Lee, K.S. / Bumbaca, D. / Kosman, J. / Setlow, P. / Jedrzejas, M.J.
History
DepositionJun 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: 5'-D(*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*A)-3'
E: 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*A)-3'
A: Small, acid-soluble spore protein C
B: Small, acid-soluble spore protein C
C: Small, acid-soluble spore protein C


Theoretical massNumber of molelcules
Total (without water)26,7415
Polymers26,7415
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.962, 86.962, 144.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*A)-3'


Mass: 3560.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*A)-3'


Mass: 3160.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Small, acid-soluble spore protein C / SASP


Mass: 6673.570 Da / Num. of mol.: 3 / Fragment: alpha/beta-type / Mutation: N13A, D14K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: sspC / Plasmid: pPS708 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02958
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01M magnesium sulfate, 0.05M sodium cacodylate, 1.4M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium sulfate11
2sodium cacodylate11
3ammonium sulfate11
4H2O11
5magnesium sulfate12
6odium cacodylate12
7ammonium sulfate12
8H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111.1
SYNCHROTRONALS 8.2.120.9799, 0.9800, 0.9574
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 3, 2003
ADSC QUANTUM 2102CCDJul 3, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si (111)SINGLE WAVELENGTHMx-ray1
2Double crystal, Si (111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97991
30.981
40.95741
ReflectionResolution: 2.1→50 Å / Num. all: 18561 / Num. obs: 17711 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1144 / Rsym value: 0.292 / % possible all: 59.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→27.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 31089.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 853 4.8 %RANDOM
Rwork0.257 ---
obs0.257 17708 90.7 %-
all-18561 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4873 Å2 / ksol: 0.382571 e/Å3
Displacement parametersBiso mean: 60.9 Å2
Baniso -1Baniso -2Baniso -3
1--11.18 Å2-4.52 Å20 Å2
2---11.18 Å20 Å2
3---22.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 446 0 22 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 105 5.2 %
Rwork0.42 1906 -
obs-2019 63.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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