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- PDB-4itq: Crystal structure of hypothetical protein SCO1480 bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4itq
TitleCrystal structure of hypothetical protein SCO1480 bound to DNA
Components
  • 5'-D(P*CP*CP*GP*CP*GP*CP*GP*C)-3'
  • 5'-D(P*GP*CP*GP*CP*GP*CP*GP*G)-3'
  • Putative uncharacterized protein SCO1480
KeywordsGENE REGULATION / STRUCTURAL PROTEIN/DNA / protein-DNA complex / H2TH motif / nucleoid-associated protein / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


nucleoid / chromosome condensation / DNA binding / cytoplasm
Similarity search - Function
: / : / S13-like H2TH domain / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13 family profile. / Ribosomal protein S13-like, H2TH / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Integration host factor
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGuarne, A. / Nanji, T. / Gloyd, M. / Swiercz, J.P. / Elliot, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: A novel nucleoid-associated protein specific to the actinobacteria.
Authors: Swiercz, J.P. / Nanji, T. / Gloyd, M. / Guarne, A. / Elliot, M.A.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein SCO1480
B: 5'-D(P*CP*CP*GP*CP*GP*CP*GP*C)-3'
C: 5'-D(P*GP*CP*GP*CP*GP*CP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)16,5743
Polymers16,5743
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.420, 71.782, 102.925
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 Putative uncharacterized protein SCO1480 / sIHF


Mass: 11717.030 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein is MSE-labeled / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO1480 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) pRare / References: UniProt: Q9KXR9
#2: DNA chain 5'-D(P*CP*CP*GP*CP*GP*CP*GP*C)-3'


Mass: 2388.569 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*CP*GP*CP*GP*CP*GP*G)-3'


Mass: 2468.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE CRYSTALLIZATION DROPS IS: 5' ...THE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE CRYSTALLIZATION DROPS IS: 5' GAGGGAGTGCGTGGGTCTGA 3'/5' CTCAGACCCACGCACTCCCT 3'. THE DUPLEX WAS PARTLY DISORDERED IN THE CRYSTAL STRUCTURE (PROBABLY BECAUSE THE PROTEIN BINDS DNA UNSPECIFICALLY AND COULD BIND ALL ALONG THE DUPLEX). AS A RESULT ONLY 8 BP ARE VISIBLE IN THE ASYMMETRIC UNIT. THE DENSITY COULD NOT BE ASSIGNED TO ANY PARTICULAR SEQUENCE OF THE 19 BP DUPLEX AND HENCE THE ELECTRON DENSITY WAS MODELED BASED ON THE RELATIVE SIZE OF THE NUCLEOTIDE MOIETY (USING GUANOSINE FOR "PURINE-LIKE" DENSITIES AND CYTOSINE FOR "PYRIMIDINE-LIKE" DENSITIES).

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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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 19% PEG 3350, 210 mM KSCN, 5% ethylene glycol, 100 mM HEPES pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2012 / Details: mirrors
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 5202 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.6-2.644.60.5391.4462194.7
7.05-506.50.02666.44801100
5.6-7.056.50.04847.54911100
4.89-5.66.80.0448.14751100
4.45-4.896.30.04642.14831100
4.13-4.456.80.04444.94711100
3.88-4.136.10.04541.74881100
3.69-3.886.60.06128.64691100
3.53-3.696.60.05728.54771100
3.39-3.536.60.04134.74761100
3.28-3.395.80.04925475199.8
3.17-3.286.20.04322.94751100
3.08-3.176.40.05614.94801100
3-3.086.20.1886.14731100
2.93-35.70.2664.64971100
2.86-2.935.90.3543.44721100
2.8-2.8660.33.44621100
2.74-2.86.10.4662.54921100
2.69-2.745.80.4632.3478199
2.64-2.695.10.5561.7449198

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Processing

Software
NameVersionClassification
CBASSdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→29.439 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.315 447 9.69 %random
Rwork0.2617 ---
obs0.2672 4613 98.91 %-
all-4664 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.37 Å2 / ksol: 0.265 e/Å3
Displacement parametersBiso mean: 67.32 Å2
Baniso -1Baniso -2Baniso -3
1-29.9819 Å2-0 Å2-0 Å2
2---13.1865 Å2-0 Å2
3----18.3995 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 328 0 6 992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031042
X-RAY DIFFRACTIONf_angle_d0.7891464
X-RAY DIFFRACTIONf_dihedral_angle_d22.447421
X-RAY DIFFRACTIONf_chiral_restr0.038168
X-RAY DIFFRACTIONf_plane_restr0.001136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7001-3.09040.41791410.36791349134998
3.0904-3.89220.32761490.24281362136299
3.8922-29.44040.29031570.250114551455100

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