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- PDB-7xgs: Short vegetative phase protein -

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Basic information

Entry
Database: PDB / ID: 7xgs
TitleShort vegetative phase protein
ComponentsMADS-box protein SVP
KeywordsGENE REGULATION / helix-loop-helix / RNA / plant phenotype
Function / homology
Function and homology information


negative regulation of flower development / flower development / response to temperature stimulus / mRNA regulatory element binding translation repressor activity / sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...negative regulation of flower development / flower development / response to temperature stimulus / mRNA regulatory element binding translation repressor activity / sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription factor, K-box / K-box region / K-box domain profile. / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS
Similarity search - Domain/homology
MADS-box protein SVP
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsLiao, Y.-T. / Wang, H.-C. / Ko, T.-P.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2313-B-002-042 Taiwan
CitationJournal: To Be Published
Title: The PHYL1 effector of peanut witches broom (PnWB) phytoplasma alters the miR156/157-mediated squamosa promoter binding protein like regulation and gibberellic acid generation to promote anthocyanin biosynthesis
Authors: Pan, Z.-J. / Huang, Y.-C. / Cheng, H.-P. / Lin, C.-P. / Liao, Y.-T. / Ko, T.-P. / Wang, H.-C. / Lin, S.-S.
History
DepositionApr 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: 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: MADS-box protein SVP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8593
Polymers12,7341
Non-polymers1242
Water1,27971
1
A: MADS-box protein SVP
hetero molecules

A: MADS-box protein SVP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7176
Polymers25,4692
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area3590 Å2
ΔGint-25 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.617, 116.440, 50.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-202-

EDO

21A-202-

EDO

31A-337-

HOH

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Components

#1: Protein MADS-box protein SVP / / Protein SHORT VEGETATIVE PHASE


Mass: 12734.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SVP, At2g22540, F14M13.6
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9FVC1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-citrate, PEG 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 6460 / % possible obs: 98.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 26.99 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 52.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 598

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→20 Å / SU ML: 0.1772 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.0079 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2332 318 5.01 %
Rwork0.1881 8574 -
obs0.1904 6367 74.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.86 Å2
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms564 0 8 71 643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025571
X-RAY DIFFRACTIONf_angle_d0.5313751
X-RAY DIFFRACTIONf_chiral_restr0.031184
X-RAY DIFFRACTIONf_plane_restr0.005997
X-RAY DIFFRACTIONf_dihedral_angle_d22.7374371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.290.321250.247513X-RAY DIFFRACTION42
2.53-3.180.25861520.21412905X-RAY DIFFRACTION75.99
3.18-200.22262020.17293818X-RAY DIFFRACTION99.31
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)
10.9897077477570.0325825256522-0.3895551326661.87352625613-1.605221408875.39809478145-0.499044565842-1.446992448760.7460170325391.048309845040.3687221139920.287311082831-0.9671388035160.0308617530788-0.06096755876330.3063471136640.1668038997150.2015608400170.627696650777-0.1253286243870.1341494546286.6624873457334.393317486352.1791297233
23.25540087838-2.52110762626-1.176567918748.061817534542.078664453081.040230797470.290186005210.2566940057310.228663907664-0.4110646072070.0067946049875-1.25488418285-0.1061985416150.431573519212-0.09263077790980.2455946472720.0842711535811-0.02477657073110.280365662934-0.03731027498550.18893237605519.805808721617.984968776933.8043896607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 94 )

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