[English] 日本語
Yorodumi
- PDB-4z8v: CRYSTAL STRUCTURE OF AVRRXO1-ORF1:-ORF2 COMPLEX, NATIVE. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z8v
TitleCRYSTAL STRUCTURE OF AVRRXO1-ORF1:-ORF2 COMPLEX, NATIVE.
Components
  • AvrRxo1-ORF1
  • AvrRxo1-ORF2
KeywordsPROTEIN BINDING / TYPE III EFFECTOR PROTEINS / CHAPERONE
Function / homologyP-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / AvrRxo1-ORF1 / AvrRxo1-ORF2
Function and homology information
Biological speciesXanthomonas oryzae pv. oryzicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHan, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. ...Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Yang, Z. / Miao, J. / Triplett, L. / Cheng, Q. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-0845283 United States
United States Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA, United States)2011-67012-30570 United States
United States Department of Agriculture (USDA), National Institute of Food and Agriculture (NIFA, United States)2014-67013-21564 United States
National Natural Science Foundation of China (NSFC)31472186 China
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2.
Authors: Han, Q. / Zhou, C. / Wu, S. / Liu, Y. / Triplett, L. / Miao, J. / Tokuhisa, J. / Deblais, L. / Robinson, H. / Leach, J.E. / Li, J. / Zhao, B.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 16, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1578
Polymers47,5872
Non-polymers5706
Water2,810156
1
A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules

A: AvrRxo1-ORF1
B: AvrRxo1-ORF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,31316
Polymers95,1734
Non-polymers1,14012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9170 Å2
ΔGint-57 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.299, 88.390, 152.532
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-504-

PO4

21A-654-

HOH

-
Components

#1: Protein AvrRxo1-ORF1


Mass: 36203.832 Da / Num. of mol.: 1 / Fragment: unp residues 88-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR8
#2: Protein AvrRxo1-ORF2


Mass: 11382.900 Da / Num. of mol.: 1 / Fragment: unp residues 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzicola (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6TKR9
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M NAH2PO4, 0.8 M KH2PO4, 15% GLYCEROL, 8 MM DTT, 0.1 M HEPES, PH7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21791 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q5L

4q5l
PDB Unreleased entry


Resolution: 2.3→45.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1176 5.1 %RANDOM
Rwork0.202 ---
obs0.204 21791 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 30 156 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9844596
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59724150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19815609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3671526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212529
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 91 -
Rwork0.244 1575 -
obs--98.87 %

+
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