[English] 日本語
Yorodumi
- PDB-4bjm: Crystal structure of the flax-rust effector avrM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bjm
TitleCrystal structure of the flax-rust effector avrM
ComponentsAVRM
KeywordsPROTEIN TRANSPORT / PLANT DISEASES / IMMUNITY / INNATE / PROTEIN MULTIMERIZATION / PROTEIN BINDING / MEMBRANE TRANSLOCATION / STRUCTURE-ACTIVITY RELATIONSHIP VIRULENCE FACTORS
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1680 / Flax-rust effector AvrM-A / Flax-rust effector AvrM, N-terminal domain / Flax-rust effector AvrM-A / Flax-rust effector AvrM N-terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / AvrM
Function and homology information
Biological speciesMELAMPSORA LINI (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVe, T. / Williams, S.J. / Kobe, B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of the Flax-Rust Effector Avrm Reveal Insights Into the Molecular Basis of Plant-Cell Entry and Effector-Triggered Immunity
Authors: Ve, T. / Williams, S.J. / Catanzariti, A.M. / Rafiqi, M. / Rahman, M. / Ellis, J.G. / Hardham, A.R. / Jones, D.A. / Anderson, P.A. / Dodds, P.N. / Kobe, B.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and X-Ray Diffraction Analysis of the C-Terminal Domain of the Flax Rust Effector Protein Avrm.
Authors: Ve, T. / Williams, S.J. / Stamp, A. / Valkov, E. / Dodds, P.N. / Anderson, P.A. / Kobe, B.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: AVRM
B: AVRM
C: AVRM
D: AVRM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7005
Polymers109,6644
Non-polymers351
Water2,270126
1
A: AVRM
B: AVRM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8683
Polymers54,8322
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-25.3 kcal/mol
Surface area26370 Å2
MethodPISA
2
C: AVRM
D: AVRM


Theoretical massNumber of molelcules
Total (without water)54,8322
Polymers54,8322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-11.2 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.470, 125.610, 128.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
AVRM


Mass: 27416.035 Da / Num. of mol.: 4 / Fragment: RESIDUES 46-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MELAMPSORA LINI (flax rust) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2MV46
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.34 Å3/Da / Density % sol: 63.22 % / Description: NONE
Crystal growDetails: 0.1 M MES PH 6.5, 1.3 M SODIUM CITRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95394
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95394 Å / Relative weight: 1
ReflectionResolution: 2.6→72.93 Å / Num. obs: 44915 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.3 % / Biso Wilson estimate: 79.53 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BJM

4bjm


Resolution: 2.6→26.14 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.358 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.243
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2259 5.04 %RANDOM
Rwork0.2093 ---
obs0.2105 44794 99.98 %-
Displacement parametersBiso mean: 98.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.9565 Å20 Å20 Å2
2--4.3113 Å20 Å2
3----7.2679 Å2
Refine analyzeLuzzati coordinate error obs: 0.461 Å
Refinement stepCycle: LAST / Resolution: 2.6→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7092 0 1 126 7219
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017176HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.019624HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3583SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes243HARMONIC2
X-RAY DIFFRACTIONt_gen_planes997HARMONIC5
X-RAY DIFFRACTIONt_it7176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion3.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion930SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7988SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3016 156 4.81 %
Rwork0.2337 3085 -
all0.237 3241 -
obs--99.98 %
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)
10.7160.05630.72020.7901-0.31470.37930.0012-0.3375-0.17460.00510.095-0.07030.03230.135-0.0962-0.26910.00180.02110.02140.03850.067-2.057524.49590.7601
20-0.5007-0.58551.45860.36932.35070.0466-0.12630.1464-0.5442-0.00240.04770.2275-0.1727-0.04420.0912-0.01390.019-0.10950.0259-0.0529-4.02322.3193-31.6832
30.0864-0.4632-0.91013.03672.17371.45610.01760.0204-0.00830.0587-0.29690.08030.2453-0.25450.2793-0.04110.031-0.0987-0.2062-0.1508-0.1209-9.7806-5.6538-28.3784
40.2298-0.28390.01840.48610.0650.15850.03230.00130.0370.2108-0.015-0.02020.16710.0555-0.01730.17730.0538-0.0611-0.0401-0.1291-0.061113.6886-7.8685-8.0389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

+
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://pdbjlvh1.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