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- PDB-6jqa: Crystal structure of phyllogen, a phyllody inducing effector prot... -

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Basic information

Entry
Database: PDB / ID: 6jqa
TitleCrystal structure of phyllogen, a phyllody inducing effector protein of phytoplasma.
Components(Phytoplasmal effector causing phyllody 1) x 3
KeywordsTRANSCRIPTION / Phytoplasma / Phyllody / Phyllogen / PHYL1 / MADS-domain transcription factor
Function / homologySequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / IODIDE ION / Phytoplasmal effector causing phyllody 1
Function and homology information
Biological speciesOnion yellows phytoplasma OY-W (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.402 Å
AuthorsMiyatake, H. / Maejima, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25221201 Japan
Japan Society for the Promotion of ScienceGS005 Japan
Japan Society for the Promotion of Science16K14643 Japan
Japan Society for the Promotion of Science17J09944 Japan
Japan Society for the Promotion of Science17H06618 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of phyllogen, a phyllody-inducing effector protein of phytoplasma.
Authors: Iwabuchi, N. / Maejima, K. / Kitazawa, Y. / Miyatake, H. / Nishikawa, M. / Tokuda, R. / Koinuma, H. / Miyazaki, A. / Nijo, T. / Oshima, K. / Yamaji, Y. / Namba, S.
History
DepositionMar 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phytoplasmal effector causing phyllody 1
B: Phytoplasmal effector causing phyllody 1
C: Phytoplasmal effector causing phyllody 1
D: Phytoplasmal effector causing phyllody 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,47123
Polymers45,0604
Non-polymers2,41119
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-30 kcal/mol
Surface area19200 Å2
Unit cell
Length a, b, c (Å)42.843, 60.664, 124.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phytoplasmal effector causing phyllody 1


Mass: 11170.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The crystal was iodine labelled for I-SAD phasing by HYPER-VIL
Source: (gene. exp.) Onion yellows phytoplasma OY-W (bacteria)
Gene: PHYL1 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: X5IFG3
#2: Protein Phytoplasmal effector causing phyllody 1


Mass: 11422.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onion yellows phytoplasma OY-W (bacteria)
Gene: PHYL1 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: X5IFG3
#3: Protein Phytoplasmal effector causing phyllody 1


Mass: 11044.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onion yellows phytoplasma OY-W (bacteria)
Gene: PHYL1 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: X5IFG3
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100mM sodium citrate pH 5.0, 2.1M ammonium sulfate, 250mM MgCl2, 2.5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.402→43.509 Å / Num. obs: 194152 / % possible obs: 85.56 % / Redundancy: 7.9 % / Biso Wilson estimate: 44.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1374 / Rpim(I) all: 0.05178 / Rrim(I) all: 0.147 / Net I/σ(I): 8.21
Reflection shellResolution: 2.402→2.488 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.9488 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 20164 / CC1/2: 0.713 / Rpim(I) all: 0.3528 / Rrim(I) all: 1.013 / % possible all: 52.53

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3260)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.402→43.509 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3025 2093 9.98 %
Rwork0.2685 --
obs0.2719 20966 85.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.402→43.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 19 16 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162810
X-RAY DIFFRACTIONf_angle_d1.7673790
X-RAY DIFFRACTIONf_dihedral_angle_d4.1551775
X-RAY DIFFRACTIONf_chiral_restr0.063436
X-RAY DIFFRACTIONf_plane_restr0.009497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.402-2.45780.2864870.2974723X-RAY DIFFRACTION50
2.4578-2.51930.33641030.3018897X-RAY DIFFRACTION60
2.5193-2.58740.34031150.2971014X-RAY DIFFRACTION71
2.5874-2.66350.30741260.30431109X-RAY DIFFRACTION75
2.6635-2.74950.35921230.30011164X-RAY DIFFRACTION78
2.7495-2.84770.31061390.28461247X-RAY DIFFRACTION84
2.8477-2.96170.2911400.27551292X-RAY DIFFRACTION90
2.9617-3.09650.33911460.27261340X-RAY DIFFRACTION90
3.0965-3.25970.29561470.27541374X-RAY DIFFRACTION94
3.2597-3.46380.3121570.2581424X-RAY DIFFRACTION96
3.4638-3.73120.34241590.25651453X-RAY DIFFRACTION98
3.7312-4.10640.24161600.23551431X-RAY DIFFRACTION99
4.1064-4.70.2121670.21041481X-RAY DIFFRACTION100
4.7-5.91910.31441610.29921452X-RAY DIFFRACTION99
5.9191-43.51640.38681630.30821472X-RAY DIFFRACTION99
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)
13.94523.3693-0.18458.52935.89697.2925-0.2735-0.16990.1744-0.05661.0357-0.4399-0.05140.7276-0.57250.19620.05130.03730.43830.01130.2779-3.958616.1507-23.2195
24.544-2.973-1.27873.5864-0.44894.5548-0.1884-0.0235-0.7770.20810.17221.16890.5776-0.37850.14230.34-0.1011-0.04860.40960.00140.3575-9.65314.5366-20.7389
34.2164-4.302-1.95541.98531.99962.00920.1491-0.9018-0.0478-3.0444-3.17931.6106-1.6452-2.84051.55261.55020.0251-0.37960.9055-0.06891.0532-17.175233.6867-19.8949
43.98270.96990.80072.87261.0367.6970.30150.0025-0.48860.0382-0.04820.0440.1928-0.0902-0.25590.25160.0004-0.01090.3088-0.05250.46144.505412.505-24.4917
54.8184-1.5628-0.18024.31953.61494.1737-0.34820.00330.67330.4177-0.1064-0.3261-1.41610.70280.43680.9743-0.3033-0.09240.4870.00670.56019.773628.368-18.9126
64.31391.147-3.95997.1899-4.86045.74530.2634-0.2844-0.82940.08280.3974-0.36870.1439-0.86550.57150.68090.033-0.15720.57310.03351.048915.97370.5139-24.3047
70.36691.0526-1.53393.1965-4.42676.131.15492.2815-0.9330.58480.2382-0.4516-0.56423.6851-0.10250.81580.0198-0.44831.9324-0.67631.641113.6337-5.5307-11.519
85.4165-3.9074-1.39216.47362.33793.66310.1701-0.4799-0.4181-0.1794-0.06321.0453-0.3057-0.0608-0.22260.2891-0.0180.01250.4631-0.12430.5112-8.594516.5985-6.3003
97.3877-4.40810.57447.0951-2.44751.56960.2567-0.0651-1.4777-0.5578-0.18081.92910.374-0.6393-0.04090.3193-0.11570.04790.711-0.14020.5326-13.910211.8607-11.0001
102.527-2.11674.10281.9318-3.24716.70780.9183-0.4861-2.1633-1.8126-1.8787-0.37213.01952.2131-0.74211.06440.36420.23170.91270.24361.61780.4693-8.9169-9.2876
119.8375-5.30423.42984.4586-2.2166.4042-0.0063-0.49890.6414-0.11290.4588-0.431-0.0975-0.2848-0.44370.239-0.13520.06330.4392-0.08050.41991.076619.1388-6.3547
126.1563-3.1995-2.42197.82341.13056.04710.33110.3574-0.02940.1872-0.3277-1.14590.00340.4283-0.18390.2417-0.1084-0.15510.5199-0.05520.537611.63817.9636-8.5638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 91 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 90 )
7X-RAY DIFFRACTION7chain 'C' and (resid 11 through 19 )
8X-RAY DIFFRACTION8chain 'C' and (resid 20 through 54 )
9X-RAY DIFFRACTION9chain 'C' and (resid 55 through 77 )
10X-RAY DIFFRACTION10chain 'C' and (resid 78 through 90 )
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 44 )
12X-RAY DIFFRACTION12chain 'D' and (resid 45 through 90 )

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