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- PDB-2oqq: Crystal structure of HY5 leucine zipper homodimer from Arabidopsi... -

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Basic information

Entry
Database: PDB / ID: 2oqq
TitleCrystal structure of HY5 leucine zipper homodimer from Arabidopsis thaliana
ComponentsTranscription factor HY5
KeywordsTRANSCRIPTION / homodimer leucine zipper
Function / homology
Function and homology information


positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / positive regulation of flavonoid biosynthetic process / positive gravitropism / gibberellic acid mediated signaling pathway / red, far-red light phototransduction / response to far red light ...positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / positive regulation of flavonoid biosynthetic process / positive gravitropism / gibberellic acid mediated signaling pathway / red, far-red light phototransduction / response to far red light / response to abscisic acid / positive regulation of circadian rhythm / abscisic acid-activated signaling pathway / response to UV-B / response to cold / protein-DNA complex / double-stranded DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcriptional activator Hac1/HY5 / Single helix bin / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor HY5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsYoon, M.-K. / Kim, H.M. / Choi, G. / Lee, J.-O. / Choi, B.-S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis for the conformational integrity of the Arabidopsis thaliana HY5 leucine zipper homodimer.
Authors: Yoon, M.K. / Kim, H.M. / Choi, G. / Lee, J.O. / Choi, B.S.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 27, 2021Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
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 / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Transcription factor HY5
B: Transcription factor HY5


Theoretical massNumber of molelcules
Total (without water)9,9292
Polymers9,9292
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-17 kcal/mol
Surface area6160 Å2
MethodPISA
2
A: Transcription factor HY5
B: Transcription factor HY5

A: Transcription factor HY5
B: Transcription factor HY5


Theoretical massNumber of molelcules
Total (without water)19,8584
Polymers19,8584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5360 Å2
ΔGint-46 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.344, 24.583, 76.517
Angle α, β, γ (deg.)90.000, 100.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Transcription factor HY5 / Protein LONG HYPOCOL5 / AtbZIP56


Mass: 4964.506 Da / Num. of mol.: 2 / Fragment: Hy5 leucine zipper
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O24646
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris pH6.0 0.1M MgCl2 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714, 0.97880, 0.97895, 0.97114
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.127141
20.97881
30.978951
40.971141
ReflectionResolution: 2→50 Å / Num. obs: 6080 / % possible obs: 97.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.392 / Num. unique all: 553 / % possible all: 87.8

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.77 / FOM acentric: 0.78 / FOM centric: 0.74 / Reflection: 5190 / Reflection acentric: 4648 / Reflection centric: 542
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-37.6740.880.90.8324917871
3.8-60.910.910.9727607120
3-3.80.870.880.8186777394
2.6-30.810.810.7588781077
2.3-2.60.720.730.5815361421115
2.1-2.30.60.60.5592485965
Phasing MIRResolution: 2→20 Å / FOM: 0.595 / FOM acentric: 0.598 / FOM centric: 0.571 / Reflection: 5190 / Reflection acentric: 4648 / Reflection centric: 542
Phasing MIR der

Der set-ID: 1

IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
edge2-201.58100004648542
peak2-200.930.895.46.20.560.64627516
remote2-200.710.584.65.71.411.44632502
native3-200.93111.914.60.560.41755139
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
9.4120edge1.1110.10003830
6.159.41edge1.9610.100012539
4.576.15edge1.6510.100025863
3.644.57edge1.0610.10.10044669
3.023.64edge1.321000066480
2.583.02edge1.761000098696
2.252.58edge2.17100001279101
22.25edge3.191000085264
9.4120peak0.950.728.25.40.871.163829
6.159.41peak0.90.95.97.21.060.5112439
4.576.15peak0.880.726.76.30.810.9725762
3.644.57peak0.970.947.48.20.630.6244565
3.023.64peak0.921.076.460.580.6466276
2.583.02peak0.930.865.26.30.540.4698493
2.252.58peak0.930.974.54.60.480.46127396
22.25peak0.960.944.55.90.380.2984456
9.4120remote0.490.385.85.92.592.43828
6.159.41remote0.540.74.85.22.821.4812536
4.576.15remote0.60.454.84.92.462.625862
3.644.57remote0.590.484.862.111.8244668
3.023.64remote0.620.534.55.81.81.4266378
2.583.02remote0.720.714.54.91.331.2298485
2.252.58remote0.770.714.461.050.74127189
22.25remote0.880.774.86.60.760.5984756
9.4120native0.731.1711.414.51.070.532114
6.159.41native0.820.958.912.60.960.386021
4.576.15native0.8818.712.40.920.6713029
3.644.57native0.950.8913.818.20.50.3421132
3.023.64native0.951.1212.814.70.430.2831842
2.583.02native0.960.518.64.70.51.04151
2.252.58native00000000
22.25native00000000
Phasing MIR der site

Biso : 25 Å / Atom type symbol: Au

IDDer-IDFract xFract yFract zOccupancy
1edge0.4980.0640.4660
2edge0.7290.0540.4680
3peak0.4980.0630.4660.032
4peak0.7280.0540.4680.028
5remote0.4970.0620.4660.064
6remote0.7290.0530.4680.066
7native0.4970.1050.4660.045
8native0.7390.050.4680.034
Phasing MIR shell
Resolution (Å)FOMFOM acentricFOM centricReflectionReflection acentricReflection centric
9.41-200.6520.690.604683830
6.15-9.410.7370.7730.62316412539
4.57-6.150.7280.7250.73832125863
3.64-4.570.7040.7110.65851544669
3.02-3.640.7030.7070.66874466480
2.58-3.020.6240.6330.536108298696
2.25-2.580.5380.5450.43813801279101
2-2.250.4240.4250.40991685264

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RESOLVE2.09phasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: SIRAS / Resolution: 2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.296 621 10 %
Rwork0.243 --
obs-5680 91.3 %
Solvent computationBsol: 47.692 Å2
Displacement parametersBiso mean: 38.094 Å2
Baniso -1Baniso -2Baniso -3
1-1.784 Å20 Å2-4.981 Å2
2--3.952 Å20 Å2
3----5.735 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 0 102 796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.242
X-RAY DIFFRACTIONc_mcbond_it1.6071.5
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_mcangle_it2.5972
X-RAY DIFFRACTIONc_scangle_it4.0612.5
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
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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