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- PDB-1l3a: Structure of the plant transcriptional regulator PBF-2 -

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Basic information

Entry
Database: PDB / ID: 1l3a
TitleStructure of the plant transcriptional regulator PBF-2
Componentsp24: plant transcriptional regulator PBF-2
KeywordsDNA BINDING PROTEIN / PBF-2 / single strand DNA binding protein / plant / whirly / transcriptionnal activator / cyclic C4 symmetry
Function / homology
Function and homology information


defense response to fungus / chloroplast / single-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Whirly transcription factor / Whirly transcription factor / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein WHY1, chloroplastic
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDesveaux, D. / Allard, J. / Brisson, N. / Sygusch, J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A new family of plant transcription factors displays a novel ssDNA-binding surface.
Authors: Desveaux, D. / Allard, J. / Brisson, N. / Sygusch, J.
History
DepositionFeb 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p24: plant transcriptional regulator PBF-2
B: p24: plant transcriptional regulator PBF-2
C: p24: plant transcriptional regulator PBF-2
D: p24: plant transcriptional regulator PBF-2


Theoretical massNumber of molelcules
Total (without water)101,6544
Polymers101,6544
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-110 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.869, 89.807, 144.390
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
p24: plant transcriptional regulator PBF-2 / PBF-2


Mass: 25413.449 Da / Num. of mol.: 4 / Fragment: Residues 68-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Description: p24: plant transcriptional regulator PBF-2 / Plasmid: pET21a / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LL85
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 44.77 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 8
Details: 20 mM Tris/HCL, pH 8.0, SMALL TUBES, temperature 277K
Crystal grow
*PLUS
Method: eppendorf tubes
Details: Desveaux, D., (2002) Acta Crystallogr., Sect.D, 58, 296.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-15 mg/mlprotein11
220 mMTris-HCl11pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 29, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.42 Å / Num. all: 41118 / Num. obs: 35350 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 35 Å2
Reflection shellResolution: 2.3→2.44 Å / % possible all: 60.7
Reflection
*PLUS
Num. obs: 40505 / % possible obs: 98.4 % / Num. measured all: 306528 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Lowest resolution: 2.38 Å / % possible obs: 89.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→42.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 632595.99 / Data cutoff high rms absF: 632595.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3575 10.1 %RANDOM
Rwork0.216 ---
all0.2326 41118 --
obs0.216 35350 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2979 Å2 / ksol: 0.324584 e/Å3
Displacement parametersBiso mean: 56.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--9.46 Å20 Å2
3----10.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 0 477 5915
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it3.182
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.752.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 417 10.2 %
Rwork0.253 3664 -
obs-3664 60.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 10 % / Rfactor all: 0.2326 / Rfactor obs: 0.216 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.228
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.253

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