[English] 日本語
Yorodumi
- PDB-4fcg: Structure of the leucine-rich repeat domain of the type III effec... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Chloride


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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more