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- PDB-7vsq: Crystal strcuture of the tandem B-Box domains of CONSTANS -

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Basic information

Entry
Database: PDB / ID: 7vsq
TitleCrystal strcuture of the tandem B-Box domains of CONSTANS
ComponentsZinc finger protein CONSTANS
KeywordsPLANT PROTEIN / B-Box / CONSTANS / Photoperiod
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiu, R. / Lv, X. / 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,86415
Polymers33,0793
Non-polymers78512
Water32418
1
A: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2885
Polymers11,0261
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6000 Å2
MethodPISA
2
B: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2885
Polymers11,0261
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-2 kcal/mol
Surface area5990 Å2
MethodPISA
3
C: Zinc finger protein CONSTANS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2885
Polymers11,0261
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.813, 50.813, 97.624
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Zinc finger protein CONSTANS


Mass: 11026.373 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: CO, At5g15840, F14F8_220 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q39057
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic dehydrate, pH 5.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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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: Dec 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7733 / % possible obs: 99.5 % / Redundancy: 9.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 386 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VSP

7vsp


Resolution: 2.7→32.684 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 39.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3048 354 4.62 %
Rwork0.2774 7311 -
obs0.2787 7665 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.09 Å2 / Biso mean: 95.4925 Å2 / Biso min: 34.88 Å2
Refinement stepCycle: final / Resolution: 2.7→32.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 12 18 2004
Biso mean--92.8 58.68 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112006
X-RAY DIFFRACTIONf_angle_d1.7622717
X-RAY DIFFRACTIONf_chiral_restr0.09307
X-RAY DIFFRACTIONf_plane_restr0.009366
X-RAY DIFFRACTIONf_dihedral_angle_d17.996735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7002-3.09070.33781060.3294238797
3.0907-3.8930.37761320.31562471100
3.893-32.680.26531160.24882453100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.84462.3722-0.89338.1408-0.94643.1813-0.3388-0.0531-0.16540.16040.003-0.27120.15950.67080.39990.5131-0.10040.04920.8462-0.10230.54610.5503-0.7364-6.6786
28.04031.60156.57083.3086-2.80882.03121.6343-1.5315-0.5638-0.6408-0.43930.25820.6335-0.45411.59170.83170.12390.44110.6128-0.12350.38054.0429-6.87361.9541
34.59470.13521.6735.6928-3.69995.21590.28750.3523-0.3688-1.3858-0.62641.14340.70660.4041-0.20110.40210.04510.24790.70510.05730.2021-6.6802-9.21629.7648
49.4169-4.8268-3.63333.9497-0.94986.50060.71280.5395-0.91940.54650.0635-1.16270.28541.22280.75980.7469-0.03-0.06290.86530.02961.2153-14.4466-22.9461-0.0111
52.22080.72612.21178.0231-1.79658.11010.7057-0.2149-0.06840.4561-1.19730.34592.15380.53140.26850.2917-0.0040.06710.8459-0.18910.5238-24.4192-24.15254.6193
62.30092.5348-2.57614.203-5.23957.68010.43450.2213-1.7265-0.4407-1.1765-0.4055-0.37111.33510.17280.55670.2063-0.03741.1257-0.0290.5808-17.7384-7.0468-12.7583
73.8168-1.1661-0.53754.26242.30631.2585-0.00310.9974-0.8964-0.20761.2608-0.9812-0.24451.52030.23190.6546-0.480.16431.1589-0.21840.7002-24.922-3.6929-10.3382
81.993-5.26714.77754.2624-2.32922.2882-0.83250.86572.7282-0.54930.9251-2.1603-1.5805-1.56311.18440.9203-0.1885-0.0062.03110.37831.8196-6.726313.0118-3.9096
98.01310.6964-3.82359.22473.23984.17880.413-2.09440.14850.76250.09350.3403-1.30470.1465-0.00171.12390.0466-0.14711.2753-0.0540.5467-16.027318.1908-10.7308
102.80311.531-3.86961.169-0.65442.0035-1.3273-0.6778-0.30620.8025-0.126-0.77852.19182.01930.61241.98530.21240.34052.0290.23680.6627-17.79299.2440.8406
118.03835.31681.9455.9544-1.93114.859-0.46781.27230.39660.10940.2070.542.47120.1665-0.24611.12190.18570.01410.606-0.07390.7564-28.8615.17277.6087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 58 )A17 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 72 )A59 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 105 )A73 - 105
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 40 )B19 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 61 )B41 - 61
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 99 )B62 - 99
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 105 )B100 - 105
8X-RAY DIFFRACTION8chain 'C' and (resid 20 through 29 )C20 - 29
9X-RAY DIFFRACTION9chain 'C' and (resid 30 through 58 )C30 - 58
10X-RAY DIFFRACTION10chain 'C' and (resid 59 through 70 )C59 - 70
11X-RAY DIFFRACTION11chain 'C' and (resid 71 through 105 )C71 - 105

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