[English] 日本語
Yorodumi
- PDB-1aow: ANNEXIN IV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aow
TitleANNEXIN IV
ComponentsANNEXIN IV
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / 32.5KD CALELECTRIN / ENDONEXIN I / LIPOCORTIN IV / CHROMOBINDIN IV / PROTEIN II / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex
Function / homology
Function and homology information


chondroitin sulfate binding / zymogen granule membrane / chromaffin granule membrane / negative regulation of interleukin-8 production / calcium-dependent phospholipid binding / NF-kappaB binding / Notch signaling pathway / epithelial cell differentiation / calcium-dependent protein binding / heparin binding ...chondroitin sulfate binding / zymogen granule membrane / chromaffin granule membrane / negative regulation of interleukin-8 production / calcium-dependent phospholipid binding / NF-kappaB binding / Notch signaling pathway / epithelial cell differentiation / calcium-dependent protein binding / heparin binding / carbohydrate binding / nuclear membrane / apical plasma membrane / calcium ion binding / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / cell surface / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Annexin A4 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A4 / 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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZanotti, G. / Malpeli, G. / Gliubich, F. / Folli, C. / Stoppini, M. / Olivi, L. / Savoia, A. / Berni, R.
CitationJournal: Biochem.J. / Year: 1998
Title: Structure of the trigonal crystal form of bovine annexin IV.
Authors: Zanotti, G. / Malpeli, G. / Gliubich, F. / Folli, C. / Stoppini, M. / Olivi, L. / Savoia, A. / Berni, R.
History
DepositionJul 11, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANNEXIN IV


Theoretical massNumber of molelcules
Total (without water)35,0061
Polymers35,0061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.560, 118.560, 82.233
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein ANNEXIN IV / / 32.5 KD CALELECTRIN / ENDONEXIN I


Mass: 35005.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: KIDNEY / References: UniProt: P13214

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5
Details: SITTING DROP, FROM A PROTEIN SOLUTION 10 MG/ML, IN THE PRESENCE OF 1.4 M AMMONIUM SULFATE, 10 MM BETA-MERCAPTOETHANOL, PH=5.0, vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 Mammonium sulfate1drop
350 mMTris-HCl1drop
41.4 Mammonium sulfate1reservoir
510 mM2-mercaptoethanol1reservoir
60.1 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.3
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 8114 / % possible obs: 95 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 36
Reflection shellResolution: 2.99→3.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 10 / Rsym value: 0.07 / % possible all: 75.3
Reflection
*PLUS
Highest resolution: 2.99 Å / Lowest resolution: 50 Å / % possible obs: 93 %
Reflection shell
*PLUS
Lowest resolution: 3.5 Å / % possible obs: 87 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
MARSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANN

1ann


Resolution: 3→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -11 %RANDOM
Rwork0.19 ---
obs0.19 7517 95 %-
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 0 0 3039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.99 Å / Lowest resolution: 7 Å / Num. reflection obs: 6717 / Num. reflection Rfree: 800
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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