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- PDB-7vsp: Crystal strcuture of the tandem B-Box domains of COL2 -

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Basic information

Entry
Database: PDB / ID: 7vsp
TitleCrystal strcuture of the tandem B-Box domains of COL2
ComponentsZinc finger protein CONSTANS-LIKE 2
KeywordsPLANT PROTEIN / B-Box / COL2 / Photoperiod
Function / homology
Function and homology information


regulation of flower development / chloroplast organization / 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-LIKE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLv, X. / Liu, R. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCYJ20200109110403829 China
CitationJournal: J Integr Plant Biol / Year: 2022
Title: Molecular basis of CONSTANS oligomerization in FLOWERING LOCUS T activation.
Authors: Zeng, X. / Lv, X. / Liu, R. / He, H. / Liang, S. / Chen, L. / Zhang, F. / Chen, L. / He, Y. / Du, J.
History
DepositionOct 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein CONSTANS-LIKE 2
B: Zinc finger protein CONSTANS-LIKE 2
C: Zinc finger protein CONSTANS-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,22615
Polymers39,4413
Non-polymers78512
Water2,126118
1
A: Zinc finger protein CONSTANS-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4095
Polymers13,1471
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc finger protein CONSTANS-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4095
Polymers13,1471
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc finger protein CONSTANS-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4095
Polymers13,1471
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.934, 44.478, 99.765
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Zinc finger protein CONSTANS-LIKE 2


Mass: 13146.992 Da / Num. of mol.: 3 / Fragment: Tandem B-Box domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COL2, At3g02380, F11A12.106, F11A12.7, F16B3.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96502
#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.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35% 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2020
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18763 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.18 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.056 / Rrim(I) all: 0.105 / Χ2: 0.629 / Net I/σ(I): 4.2 / Num. measured all: 124258
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.183.40.3436290.9210.2130.4020.48599.6
2.18-2.263.40.27736200.9370.1740.3280.49699.8
2.26-2.373.40.22435860.9580.1420.2660.51899.8
2.37-2.493.30.1936450.9620.1240.2270.55499.9
2.49-2.653.50.16536390.9730.1030.1950.57199.9
2.65-2.853.50.12935960.9830.080.1520.64199.9
2.85-3.143.40.10436110.9840.0660.1240.65399.9
3.14-3.593.50.08136370.9910.0510.0960.76599.9
3.59-4.523.50.06436340.9920.040.0760.87999.9
4.52-503.50.05235950.9940.0330.0610.7199.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→22.93 Å / SU ML: 0.1526 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.3147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2002 963 5.15 %
Rwork0.1788 17736 -
obs0.1799 18699 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 12 118 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222033
X-RAY DIFFRACTIONf_angle_d1.23022753
X-RAY DIFFRACTIONf_chiral_restr0.0688317
X-RAY DIFFRACTIONf_plane_restr0.0107368
X-RAY DIFFRACTIONf_dihedral_angle_d16.4956742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.24421290.19882469X-RAY DIFFRACTION97.63
2.21-2.350.20811190.17772526X-RAY DIFFRACTION99.66
2.35-2.530.19041400.17272528X-RAY DIFFRACTION99.7
2.53-2.790.19071430.17742518X-RAY DIFFRACTION99.85
2.79-3.190.21891380.17412538X-RAY DIFFRACTION99.89
3.19-4.020.19091350.17132557X-RAY DIFFRACTION99.81
4.02-22.930.19581590.1852600X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 18.5792354218 Å / Origin y: 14.4852484973 Å / Origin z: 73.4568954101 Å
111213212223313233
T0.213664512195 Å2-0.0260109521003 Å20.020415523926 Å2-0.169999239279 Å20.00215028901897 Å2--0.209101352346 Å2
L0.503205937633 °2-0.202465609001 °2-0.334894847436 °2-0.0906961153621 °20.34089575365 °2--1.25495686384 °2
S0.0073892172942 Å °-0.0188483189291 Å °-0.00372062859165 Å °-0.0319246365108 Å °-0.0231851328086 Å °-0.0375758538156 Å °-0.0655626017576 Å °-0.0431667713 Å °0.0182997740366 Å °
Refinement TLS groupSelection details: all

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