4FCG | pdb_00004fcg

Structure of the leucine-rich repeat domain of the type III effector XCV3220 (XopL)

PDB DOI: https://doi.org/10.2210/pdb4FCG/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-24 Released: 2012-06-13
Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Zimmerman, M.D., Minor, W., Joachimiak, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.226 (Depositor), 0.215 (DCC)
R-Value Work:
0.171 (Depositor), 0.167 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the leucine-rich repeat domain of the type III effector XCV3220 (XopL)

Singer, A.U., Schulze, S., Xu, X., Skarina, T., Cui, H., Egler, M., Srikumar, T., Raught, B., Savchenko, A., Bonas, U.

To be published.

Macromolecule Content

Total Structure Weight: 37.36 kDa
Atom Count: 2,590
Modeled Residue Count: 296
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A	328	Xanthomonas euvesicatoria pv. vesicatoria str. 85-10	Mutation(s): 0 Gene Names: XCV3220
UniProt
Find proteins for Q3BQL2 (Xanthomonas euvesicatoria pv. vesicatoria (strain 85-10)) Explore Q3BQL2 Go to UniProtKB: Q3BQL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3BQL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.226 (Depositor), 0.215 (DCC)
R-Value Work: 0.171 (Depositor), 0.167 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.463	α = 90
b = 95.228	β = 90
c = 115.465	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXCD	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Structure summary