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- PDB-7wsj: Crystal structure of the tandem B-box domain of Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 7wsj
TitleCrystal structure of the tandem B-box domain of Arabidopsis thaliana CONSTANS
ComponentsZinc finger protein CONSTANS
KeywordsPLANT PROTEIN / tandem b-box / Zn-coordinating motif / photoperiodic flowering
Function / homology
Function and homology information


far-red light signaling pathway / regulation of flower development / flower development / response to far red light / cell differentiation / DNA-binding transcription factor activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile.
Similarity search - Domain/homology
Zinc finger protein CONSTANS
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsDahal, P. / Pathak, D. / Kwon, E. / Kim, D.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Not funded Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of a tandem B-box domain from Arabidopsis CONSTANS.
Authors: Dahal, P. / Kwon, E. / Pathak, D. / Kim, D.Y.
History
DepositionJan 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 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: Zinc finger protein CONSTANS
B: Zinc finger protein CONSTANS
C: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,82215
Polymers36,0373
Non-polymers78512
Water1,42379
1
A: Zinc finger protein CONSTANS
B: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,54810
Polymers24,0252
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-1 kcal/mol
Surface area11480 Å2
MethodPISA
2
C: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2745
Polymers12,0121
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-2 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.090, 159.090, 55.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Zinc finger protein CONSTANS


Mass: 12012.432 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CO, At5g15840, F14F8_220 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q39057
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 1.39 M Lithium Sulfate, 4.55% MPD, 85 mM Imidazole-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1.28176 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28176 Å / Relative weight: 1
ReflectionResolution: 2.4→45.93 Å / Num. obs: 19958 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.584 / Num. unique obs: 2059 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→45.93 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 954 4.79 %
Rwork0.204 18981 -
obs0.2055 19935 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.34 Å2 / Biso mean: 59.3381 Å2 / Biso min: 23.16 Å2
Refinement stepCycle: final / Resolution: 2.4→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 12 79 2191
Biso mean--77.75 52.95 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.530.31871550.28282638279397
2.53-2.680.26181360.25072733286999
2.68-2.890.31131520.24832743289599
2.89-3.180.25481300.23942708283898
3.18-3.640.2461420.20212714285699
3.64-4.590.19771290.1812727285698
4.59-45.930.19191100.1732718282897
Refinement TLS params.Method: refined / Origin x: 36.2184 Å / Origin y: 23.3896 Å / Origin z: 26.3455 Å
111213212223313233
T0.5161 Å20.0717 Å2-0.0361 Å2-0.356 Å2-0.072 Å2--0.4585 Å2
L0.7914 °2-0.0557 °2-0.6005 °2-1.1735 °20.4222 °2--0.8077 °2
S-0.1291 Å °0.1278 Å °-0.3984 Å °0.1482 Å °0.0135 Å °-0.0832 Å °0.4477 Å °0.0653 Å °0.0761 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 109
2X-RAY DIFFRACTION1allB17 - 109
3X-RAY DIFFRACTION1allC17 - 109
4X-RAY DIFFRACTION1allD1 - 12
5X-RAY DIFFRACTION1allS1 - 79

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