[English] 日本語
Yorodumi
- PDB-1ycn: X-RAY STRUCTURE OF ANNEXIN FROM ARABIDOPSIS THALIANA GENE AT1G35720 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ycn
TitleX-RAY STRUCTURE OF ANNEXIN FROM ARABIDOPSIS THALIANA GENE AT1G35720
Componentsputative Ca2+-dependent membrane-binding protein annexin
KeywordsMETAL BINDING PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural GENOMICS / CESG / AT1G35720 / ANNEXIN / MEMBRANE-BINDING / CALCIUM-BINDING
Function / homology
Function and homology information


phloem sucrose unloading / root hair tip / primary root development / plant-type cell wall / potassium ion export across plasma membrane / response to water deprivation / response to abscisic acid / plasmodesma / plant-type vacuole / apoplast ...phloem sucrose unloading / root hair tip / primary root development / plant-type cell wall / potassium ion export across plasma membrane / response to water deprivation / response to abscisic acid / plasmodesma / plant-type vacuole / apoplast / thylakoid / calcium-dependent phospholipid binding / response to osmotic stress / chloroplast stroma / response to salt stress / response to cold / chloroplast / calcium ion transmembrane transport / peroxidase activity / response to heat / copper ion binding / calcium ion binding / protein homodimerization activity / mitochondrion / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
Annexin D, plant / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin D, plant / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF ANNEXIN FROM ARABIDOPSIS THALIANA GENE AT1G35720
Authors: Center for Eukaryotic Structural Genomics (CESG)
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative Ca2+-dependent membrane-binding protein annexin
B: putative Ca2+-dependent membrane-binding protein annexin


Theoretical massNumber of molelcules
Total (without water)72,4252
Polymers72,4252
Non-polymers00
Water5,062281
1
A: putative Ca2+-dependent membrane-binding protein annexin


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative Ca2+-dependent membrane-binding protein annexin


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.543, 96.936, 226.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein putative Ca2+-dependent membrane-binding protein annexin


Mass: 36212.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT1G35720 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: GenBank: 12083278, UniProt: Q9SYT0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / pH: 8
Details: 10 MG/ML PROTEIN, 15% PEG4K, 10% MPD, 0.100 M HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97942
DetectorType: APS-1 / Detector: CCD / Date: Dec 15, 2004
Details: SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR: WATER COOLED; SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.508→33.125 Å / Num. obs: 27985 / % possible obs: 95.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.618
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 3 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.589 / % possible all: 76.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å33.13 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREP8.2.01version5.0:04/07/04phasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N00

1n00


Resolution: 2.51→33.12 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Details: MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1320 4.9 %RANDOM
Rwork0.22 ---
obs0.22 27131 93.5 %-
all-29016 --
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 38.55 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-10.98 Å20 Å20 Å2
2---2.76 Å20 Å2
3----8.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.51→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4973 0 0 281 5254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.51→2.62 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.302 160 5.2 %
Rwork0.279 2903 -
obs--85.5 %

+
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