[English] 日本語
Yorodumi
- PDB-5y96: Crystal structure of ANXUR1 extracellular domain from Arabidopsis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y96
TitleCrystal structure of ANXUR1 extracellular domain from Arabidopsis thaliana
Components(Receptor-like protein kinase ANXUR1) x 2
KeywordsTRANSFERASE / receptor-like kinase
Function / homology
Function and homology information


pollen tube tip / transmembrane receptor protein tyrosine kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-like protein kinase ANXUR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDu, S. / Xiao, J.Y.
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structures of the extracellular domains of the CrRLK1L receptor-like kinases ANXUR1 and ANXUR2
Authors: Du, S. / Qu, L.J. / Xiao, J.
History
DepositionAug 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor-like protein kinase ANXUR1
B: Receptor-like protein kinase ANXUR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4999
Polymers85,5442
Non-polymers1,9557
Water14,934829
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint38 kcal/mol
Surface area34670 Å2
Unit cell
Length a, b, c (Å)54.679, 68.740, 70.327
Angle α, β, γ (deg.)88.95, 75.00, 72.18
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Receptor-like protein kinase ANXUR1


Mass: 42835.949 Da / Num. of mol.: 1 / Fragment: UNP residues 27-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX1, At3g04690, F7O18.16 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9SR05, non-specific serine/threonine protein kinase
#2: Protein Receptor-like protein kinase ANXUR1


Mass: 42707.820 Da / Num. of mol.: 1 / Fragment: UNP residues 28-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX1, At3g04690, F7O18.16 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9SR05, non-specific serine/threonine protein kinase
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate,0.1M HEPES pH 7.5,25%(w/v) Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 83947 / % possible obs: 96.5 % / Redundancy: 3.5 % / Net I/σ(I): 17.3

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SOLVEphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y92

5y92


Resolution: 1.8→43.339 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2743 3.27 %
Rwork0.1819 --
obs0.1826 83876 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 126 829 6958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036311
X-RAY DIFFRACTIONf_angle_d0.5718571
X-RAY DIFFRACTIONf_dihedral_angle_d3.0773736
X-RAY DIFFRACTIONf_chiral_restr0.046973
X-RAY DIFFRACTIONf_plane_restr0.0041097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.83090.26991400.21483913X-RAY DIFFRACTION93
1.8309-1.86420.28151360.214022X-RAY DIFFRACTION96
1.8642-1.90.24511440.20554061X-RAY DIFFRACTION96
1.9-1.93880.2471230.20644030X-RAY DIFFRACTION96
1.9388-1.9810.25891370.19944047X-RAY DIFFRACTION96
1.981-2.02710.22561540.1994081X-RAY DIFFRACTION96
2.0271-2.07780.22071300.19444035X-RAY DIFFRACTION96
2.0778-2.13390.22461490.19764033X-RAY DIFFRACTION97
2.1339-2.19670.20461220.19874072X-RAY DIFFRACTION96
2.1967-2.26760.21341320.19434102X-RAY DIFFRACTION96
2.2676-2.34870.22031390.1964033X-RAY DIFFRACTION97
2.3487-2.44270.25131380.20144077X-RAY DIFFRACTION96
2.4427-2.55390.22921410.19884066X-RAY DIFFRACTION96
2.5539-2.68850.22651420.19424058X-RAY DIFFRACTION97
2.6885-2.85690.22971320.1964087X-RAY DIFFRACTION96
2.8569-3.07740.19911400.18934079X-RAY DIFFRACTION97
3.0774-3.3870.19251370.18034092X-RAY DIFFRACTION97
3.387-3.87680.16751360.16114132X-RAY DIFFRACTION97
3.8768-4.88330.16391310.14624037X-RAY DIFFRACTION96
4.8833-43.35180.18161400.17024076X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -20.7447 Å / Origin y: -108.3115 Å / Origin z: -156.5416 Å
111213212223313233
T0.1516 Å2-0.0304 Å20.0177 Å2-0.1344 Å2-0.0024 Å2--0.1304 Å2
L0.6073 °2-0.0066 °20.271 °2-0.1718 °20.0114 °2--0.4102 °2
S-0.0291 Å °0.023 Å °0.0106 Å °-0.0027 Å °0.0068 Å °-0.0161 Å °-0.0145 Å °-0.0126 Å °0.021 Å °
Refinement TLS groupSelection details: all

+
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