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- PDB-7qce: Crystal structure of an atypical PHD finger of VIN3 -

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Basic information

Entry
Database: PDB / ID: 7qce
TitleCrystal structure of an atypical PHD finger of VIN3
ComponentsVIN3 (Protein VERNALIZATION INSENSITIVE 3)
KeywordsNUCLEAR PROTEIN / PHD finger / four-helix bundle / histone H3 tail binding / Polycomb silencing / plant vernalisation / VIN3
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPhoenix dactylifera (date palm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsFranco-Echevarria, E. / Fiedler, M. / Dean, C. / Bienz, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192713 United Kingdom
Royal SocietyRP/R1/180002 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Plant vernalization proteins contain unusual PHD superdomains without histone H3 binding activity.
Authors: Franco-Echevarria, E. / Rutherford, T.J. / Fiedler, M. / Dean, C. / Bienz, M.
History
DepositionNov 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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: VIN3 (Protein VERNALIZATION INSENSITIVE 3)
B: VIN3 (Protein VERNALIZATION INSENSITIVE 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9909
Polymers46,4502
Non-polymers5397
Water93752
1
A: VIN3 (Protein VERNALIZATION INSENSITIVE 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6346
Polymers23,2251
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VIN3 (Protein VERNALIZATION INSENSITIVE 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3563
Polymers23,2251
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.641, 58.641, 225.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

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Components

#1: Protein VIN3 (Protein VERNALIZATION INSENSITIVE 3)


Mass: 23225.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phoenix dactylifera (date palm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.06M Morpheus Divalents, 1.1M Morpheus Buffer System pH 6.5, 10% PEG 20K, 20% PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→50.84 Å / Num. obs: 27349 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2183 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
SHELXDphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→50.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.446 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1440 5.3 %RANDOM
Rwork0.23017 ---
obs0.23198 25824 99.93 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.149 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0.56 Å2-0 Å2
2---1.12 Å20 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 19 52 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0182705
X-RAY DIFFRACTIONr_bond_other_d0.0010.022618
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9053658
X-RAY DIFFRACTIONr_angle_other_deg0.992.7556061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9945338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18422.586116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.271514
X-RAY DIFFRACTIONr_chiral_restr0.0590.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_mcbond_it7.663.1041361
X-RAY DIFFRACTIONr_mcbond_other7.6683.1021360
X-RAY DIFFRACTIONr_mcangle_it7.9654.6431696
X-RAY DIFFRACTIONr_mcangle_other7.9654.6451697
X-RAY DIFFRACTIONr_scbond_it12.0454.1041344
X-RAY DIFFRACTIONr_scbond_other12.0434.1051345
X-RAY DIFFRACTIONr_scangle_other14.0085.6671963
X-RAY DIFFRACTIONr_long_range_B_refined14.56738.1222963
X-RAY DIFFRACTIONr_long_range_B_other14.57838.0642959
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 95 -
Rwork0.328 1877 -
obs--100 %
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)
14.2409-0.69240.60691.6133-0.32021.4951-0.00840.11970.17110.09820.03480.0272-0.01080.0311-0.02650.1491-0.00030.00510.26650.08290.0329-0.7916.919-27.697
23.32281.15010.54892.2383-0.51822.37340.0367-0.0978-0.03750.14240.01410.0286-0.0419-0.011-0.05080.13530.0195-0.00670.22680.05320.01527.2624.935-12.382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A135 - 321
2X-RAY DIFFRACTION2B156 - 320

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