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- PDB-4rl5: Crystal structure of the Arabidopsis exocyst subunit exo70 family... -

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Basic information

Entry
Database: PDB / ID: 4rl5
TitleCrystal structure of the Arabidopsis exocyst subunit exo70 family protein A1
ComponentsExocyst complex component EXO70A1Exocyst
KeywordsPROTEIN BINDING / exocyst complex
Function / homology
Function and homology information


xylem vessel member cell differentiation / protoxylem development / regulation of secondary cell wall biogenesis / regulation of exocyst localization / xylem development / phragmoplast / exocyst / cell wall / exocytosis / cytoplasmic vesicle ...xylem vessel member cell differentiation / protoxylem development / regulation of secondary cell wall biogenesis / regulation of exocyst localization / xylem development / phragmoplast / exocyst / cell wall / exocytosis / cytoplasmic vesicle / cytoskeleton / extracellular region / plasma membrane / cytosol
Similarity search - Function
Exocyst complex component Exo70 / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / Cullin repeat-like-containing domain superfamily / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component EXO70A1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsZhang, Z.-M. / Zhang, C. / Song, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis.
Authors: Zhang, C. / Brown, M.Q. / van de Ven, W. / Zhang, Z.M. / Wu, B. / Young, M.C. / Synek, L. / Borchardt, D. / Harrison, R. / Pan, S. / Luo, N. / Huang, Y.M. / Ghang, Y.J. / Ung, N. / Li, R. / ...Authors: Zhang, C. / Brown, M.Q. / van de Ven, W. / Zhang, Z.M. / Wu, B. / Young, M.C. / Synek, L. / Borchardt, D. / Harrison, R. / Pan, S. / Luo, N. / Huang, Y.M. / Ghang, Y.J. / Ung, N. / Li, R. / Isley, J. / Morikis, D. / Song, J. / Guo, W. / Hooley, R.J. / Chang, C.E. / Yang, Z. / Zarsky, V. / Muday, G.K. / Hicks, G.R. / Raikhel, N.V.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exocyst complex component EXO70A1
B: Exocyst complex component EXO70A1


Theoretical massNumber of molelcules
Total (without water)129,7612
Polymers129,7612
Non-polymers00
Water0
1
A: Exocyst complex component EXO70A1


Theoretical massNumber of molelcules
Total (without water)64,8811
Polymers64,8811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Exocyst complex component EXO70A1


Theoretical massNumber of molelcules
Total (without water)64,8811
Polymers64,8811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.108, 72.117, 327.930
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 Exocyst complex component EXO70A1 / Exocyst / AtExo70a1 / Exocyst subunit Exo70 family protein A1


Mass: 64880.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EXO70A1, At5g03540, F12E4.320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LZD3

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM di-ammonium tartrate, pH7.0, and 21.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 27255 / Num. obs: 27255 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
AutoSolphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→48.521 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 44.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3479 3306 7.32 %
Rwork0.324 --
obs0.3258 45192 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 0 0 0 6415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036521
X-RAY DIFFRACTIONf_angle_d0.8188890
X-RAY DIFFRACTIONf_dihedral_angle_d13.8052098
X-RAY DIFFRACTIONf_chiral_restr0.031086
X-RAY DIFFRACTIONf_plane_restr0.0031150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.14440.57841300.50731672X-RAY DIFFRACTION93
3.1444-3.19130.53041320.451672X-RAY DIFFRACTION96
3.1913-3.24120.45281370.42671800X-RAY DIFFRACTION97
3.2412-3.29430.35791400.38831674X-RAY DIFFRACTION97
3.2943-3.35110.44981340.39731712X-RAY DIFFRACTION98
3.3511-3.4120.46271420.3891756X-RAY DIFFRACTION99
3.412-3.47760.4111420.36981751X-RAY DIFFRACTION99
3.4776-3.54860.34341370.35921725X-RAY DIFFRACTION99
3.5486-3.62570.34081440.34181788X-RAY DIFFRACTION99
3.6257-3.710.42451350.36851717X-RAY DIFFRACTION99
3.71-3.80280.39171400.35691783X-RAY DIFFRACTION99
3.8028-3.90550.44831410.31981741X-RAY DIFFRACTION99
3.9055-4.02040.38611330.33711753X-RAY DIFFRACTION99
4.0204-4.15010.36321380.33031751X-RAY DIFFRACTION99
4.1501-4.29830.34221360.29241788X-RAY DIFFRACTION99
4.2983-4.47030.35391320.29421730X-RAY DIFFRACTION99
4.4703-4.67360.27651410.29451745X-RAY DIFFRACTION98
4.6736-4.91980.30611450.28661736X-RAY DIFFRACTION99
4.9198-5.22770.41911290.30161748X-RAY DIFFRACTION99
5.2277-5.63080.31341450.36821792X-RAY DIFFRACTION100
5.6308-6.19640.45481400.37551764X-RAY DIFFRACTION100
6.1964-7.09070.35151360.3671766X-RAY DIFFRACTION100
7.0907-8.92440.24581440.28111775X-RAY DIFFRACTION100
8.9244-48.52720.2761330.25741747X-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)
12.26431.72460.91352.08110.81240.3811-0.53551.15260.2206-0.50720.3533-0.3925-0.29411.4218-0.15581.6689-0.3977-0.38223.285-0.33980.22119.4735-16.2324-111.8568
20.14030.71060.18791.8914-0.95021.35110.11011.0358-0.3258-0.7462-0.35560.39520.1044-0.4240.02081.0436-0.0133-0.06172.4321-0.11810.725710.9559-19.027-74.0363
30.49551.1863-0.43820.2244-0.73197.98480.30210.64940.124-0.1797-0.09730.1051-1.10630.3103-0.01690.58280.1514-0.00551.0653-0.02290.7116.8734-17.208-27.7918
44.1073-0.59510.07482.80922.5142.4907-0.1854-0.3738-0.4410.20990.350.0020.6389-0.406-0.35490.6814-0.0543-0.07280.848-0.03120.580510.7457-30.25567.9939
53.5526-0.3371-1.38491.31840.29075.06790.4189-0.7498-0.05020.5569-0.3530.02830.0597-0.4833-0.04221.2573-0.3070.08811.3986-0.12270.669611.666417.529615.0168
60.48130.3880.43411.77931.97345.574-0.14430.1179-0.0695-0.1408-0.11280.3121-0.0523-0.65550.13921.1494-0.13010.07341.3963-0.15920.76649.859412.5007-21.4092
71.69970.124-1.46851.1471-0.63091.5468-0.0775-1.5034-0.80650.4273-0.4033-0.9822-0.40861.28620.04061.080.0023-0.2610.90780.00071.324314.91359.5091-48.414
81.99640.592-2.85423.3623-1.53074.24540.31550.5130.42160.4429-0.32810.3330.25750.74860.18380.6341-0.0704-0.162.1403-0.14850.841514.55367.593-62.0778
90.91950.1391-1.27394.1432-1.26764.33890.19080.7612-0.2973-1.18240.31810.0930.5224-0.16530.33071.02860.2163-0.1443.260.01180.829313.34418.1223-85.9693
100.1476-0.41620.80211.2351-2.33964.3169-0.47941.2691-0.15820.594-0.71330.3982-0.96851.0263-0.1790.988-0.38360.1011.8621-0.08841.012217.81316.356-87.7198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 319 )
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 544 )
4X-RAY DIFFRACTION4chain 'A' and (resid 545 through 629 )
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 223 )
6X-RAY DIFFRACTION6chain 'B' and (resid 224 through 388 )
7X-RAY DIFFRACTION7chain 'B' and (resid 389 through 436 )
8X-RAY DIFFRACTION8chain 'B' and (resid 437 through 493 )
9X-RAY DIFFRACTION9chain 'B' and (resid 494 through 566 )
10X-RAY DIFFRACTION10chain 'B' and (resid 567 through 629 )

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