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- PDB-4fcg: Structure of the leucine-rich repeat domain of the type III effec... -

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Basic information

Entry
Database: PDB / ID: 4fcg
TitleStructure of the leucine-rich repeat domain of the type III effector XCV3220 (XopL)
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / LRR / N- and C-terminal helices / type III effector / secreted into plant host
Function / homology
Function and homology information


: / Type III effector Xcv3220, C-terminal domain / : / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Type III effector Xcv3220-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. vesicatoria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSinger, A.U. / Xu, X. / Cui, H. / Zimmerman, M.D. / Minor, W. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the leucine-rich repeat domain of the type III effector XCV3220 (XopL)
Authors: Singer, A.U. / Schulze, S. / Xu, X. / Skarina, T. / Cui, H. / Egler, M. / Srikumar, T. / Raught, B. / Savchenko, A. / Bonas, U.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3609
Polymers36,8721
Non-polymers4898
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.463, 95.228, 115.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-505-

PO4

21A-507-

PO4

31A-716-

HOH

Detailsauthors state that gel filtration of this fragment was done and the results were consistent with a monomeric protein

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Components

#1: Protein uncharacterized protein


Mass: 36871.570 Da / Num. of mol.: 1 / Fragment: UNP residues 144-450
Source method: isolated from a genetically manipulated source
Details: type III effector
Source: (gene. exp.) Xanthomonas campestris pv. vesicatoria (bacteria)
Strain: 85-10 / Gene: XCV3220 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q3BQL2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.2M Potassium sulfate, 20% PEG3350, cryoprotected with 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 20, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19233 / Num. obs: 19207 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 38.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.9 / Num. unique all: 912 / Rsym value: 0.364 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXCDphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→29.932 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 986 5.16 %random
Rwork0.1708 ---
obs0.1736 19119 99.61 %-
all-19233 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.004 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.1359 Å20 Å2-0 Å2
2--0.5667 Å20 Å2
3----0.7026 Å2
Refinement stepCycle: LAST / Resolution: 2→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 23 160 2488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072475
X-RAY DIFFRACTIONf_angle_d1.0713390
X-RAY DIFFRACTIONf_dihedral_angle_d13.165943
X-RAY DIFFRACTIONf_chiral_restr0.073388
X-RAY DIFFRACTIONf_plane_restr0.005450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0003-2.10580.31241270.22112547267499
2.1058-2.23770.26911490.17412529267899
2.2377-2.41040.24141390.178225552694100
2.4104-2.65280.25581310.171425892720100
2.6528-3.03630.23251530.170725682721100
3.0363-3.82420.19711480.150926162764100
3.8242-29.93550.20621390.173227292868100
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)
11.3687-0.43720.28321.0577-0.55670.293-0.05840.007-0.28940.18510.1335-0.35350.3580.1558-0.07140.24150.0626-0.00220.2432-0.00380.21428.5277-0.887116.2458
22.3026-1.3211-0.32754.41082.12755.5824-0.06390.0213-0.25890.0706-0.03890.19090.0997-0.11060.09970.0855-0.02590.01240.13650.00840.1392-2.909213.725115.5386
31.03330.1056-0.53852.9107-1.77561.78370.03360.14780.122-0.1636-0.0801-0.17450.0050.14370.02880.116-0.013-0.01550.18730.01560.16653.700122.3885-5.5653
42.29220.50690.79343.52080.58164.1491-0.10290.3030.5672-0.38190.03110.135-0.7549-0.36180.06950.30190.06290.0220.22550.10050.3223-2.196743.9004-15.8396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 139:163)
2X-RAY DIFFRACTION2chain 'A' and (resseq 164:221)
3X-RAY DIFFRACTION3chain 'A' and (resseq 222:372)
4X-RAY DIFFRACTION4chain 'A' and (resseq 373:437)

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