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- PDB-5itj: The structure of histone-like protein -

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Basic information

Entry
Database: PDB / ID: 5itj
TitleThe structure of histone-like protein
ComponentsAbrB family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Histone-like protein / Complex / DNA-binding fold
Function / homology
Function and homology information


: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 1.63 Å
AuthorsLin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J.
CitationJournal: PLoS ONE / Year: 2017
Title: The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA.
Authors: Lin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: AbrB family transcriptional regulator
B: AbrB family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2437
Polymers12,5672
Non-polymers6775
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-54 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.464, 48.538, 55.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AbrB family transcriptional regulator / Histone-like protein


Mass: 6283.376 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SULA_1064, SULB_1065, SULC_1064 / Plasmid: pET-29a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3K9N8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.1 M Tris-Cl, 40% PEG 400, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. obs: 14365 / % possible obs: 97.7 % / Redundancy: 8 % / Net I/σ(I): 44.7
Reflection shellResolution: 1.63→1.69 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.54 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22875 726 5.1 %RANDOM
Rwork0.17826 ---
obs0.18099 13605 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 39 153 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02812
X-RAY DIFFRACTIONr_bond_other_d0.0050.02848
X-RAY DIFFRACTIONr_angle_refined_deg2.6392.0211084
X-RAY DIFFRACTIONr_angle_other_deg1.1763.0121954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.952594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.51425.88234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82115162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.334154
X-RAY DIFFRACTIONr_chiral_restr0.150.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3071.54382
X-RAY DIFFRACTIONr_mcbond_other2.2771.533381
X-RAY DIFFRACTIONr_mcangle_it3.4482.287474
X-RAY DIFFRACTIONr_mcangle_other3.4572.293475
X-RAY DIFFRACTIONr_scbond_it4.3132.254430
X-RAY DIFFRACTIONr_scbond_other4.3162.255431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2913.115611
X-RAY DIFFRACTIONr_long_range_B_refined8.53116.101964
X-RAY DIFFRACTIONr_long_range_B_other8.52916.139965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 47 -
Rwork0.234 961 -
obs--94.83 %

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