[English] 日本語
Yorodumi
- PDB-4evf: Crystal structure of apo alpha-1 giardin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4evf
TitleCrystal structure of apo alpha-1 giardin
ComponentsGiardin subunit alpha-1
KeywordsMETAL BINDING PROTEIN / Annexin / Calcium-binding protein / membrane-binding protein
Function / homology
Function and homology information


calcium-dependent phospholipid binding / cytoskeleton organization / microtubule / calcium ion binding / cytoplasm
Similarity search - Function
Alpha giardin / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Giardin subunit alpha-1
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWeeratunga, S. / Hofmann, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Alpha-1 giardin is an annexin with highly unusual calcium-regulated mechanisms
Authors: Weeratunga, S.K. / Osman, A. / Hu, N.-J. / Wang, C.K. / Mason, L. / Svard, S. / Hope, G. / Jones, M.K. / Hofmann, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Giardin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)33,9421
Polymers33,9421
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.267, 58.747, 99.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Giardin subunit alpha-1 / alpha-1 giardin


Mass: 33941.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Plasmid: pRSET_6c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17063
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.2144.39THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS.
2
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MgCl2, 30% PEG 2000, 20mM KH2PO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX10.111.488
SYNCHROTRONAustralian Synchrotron MX221.25474, 1.25418, 1.37756
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 17, 2006
ADSC QUANTUM 315r2CCDOct 11, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
21.254741
31.254181
41.377561
ReflectionResolution: 1.9→50 Å / Num. obs: 47848 / % possible obs: 0.983 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.123
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Num. unique all: 3386 / Rsym value: 0.382 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→24.826 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.29 / σ(F): 1.39 / Phase error: 25.92 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 2252 5.11 %Random
Rwork0.1994 ---
obs0.2026 44056 96.18 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.106 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 55.04 Å2 / Biso mean: 26.3783 Å2 / Biso min: 13.13 Å2
Baniso -1Baniso -2Baniso -3
1-7.0012 Å2-0 Å20 Å2
2---7.6498 Å2-0 Å2
3---0.6485 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 286 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072417
X-RAY DIFFRACTIONf_angle_d0.9723251
X-RAY DIFFRACTIONf_dihedral_angle_d15.221913
X-RAY DIFFRACTIONf_chiral_restr0.07344
X-RAY DIFFRACTIONf_plane_restr0.004419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94130.38151490.3022496264593
1.9413-1.98640.37281210.27392537265893
1.9864-2.03610.32111540.25122559271393
2.0361-2.09110.28611290.22742518264795
2.0911-2.15260.26321360.22922592272894
2.1526-2.22210.271260.2272615274195
2.2221-2.30140.32681490.22892602275197
2.3014-2.39350.31121670.22262583275096
2.3935-2.50230.28821330.23952665279897
2.5023-2.63410.3221700.2082634280498
2.6341-2.7990.25841360.20962729286599
2.799-3.01470.26611230.19712714283799
3.0147-3.31750.26051540.189326772831100
3.3175-3.7960.22321500.17522684283499
3.796-4.7770.19091380.14652678281698
4.777-24.82820.25011170.18912521263892

+
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