[English] 日本語
Yorodumi
- PDB-3evp: crystal structure of circular-permutated EGFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3evp
Titlecrystal structure of circular-permutated EGFP
ComponentsGreen fluorescent protein,Green fluorescent protein
KeywordsSIGNALING PROTEIN / circular-permutated / EGFP / Chromophore / Luminescence / Photoprotein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.453 Å
AuthorsWang, Q. / Shui, B. / Kotlikoff, M.I. / Sondermann, H.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for Calcium Sensing by GCaMP2.
Authors: Wang, Q. / Shui, B. / Kotlikoff, M.I. / Sondermann, H.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 19, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,3491
Polymers27,3491
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 62.220, 69.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Green fluorescent protein,Green fluorescent protein


Mass: 27348.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein contains the M13 fragment of myosin light chain kinase, circular permuted EGFP from Aequorea victoria (Jellyfish), calmodulin from Rattus norvegicus (Rat)
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE THE CHROMOPHORE ...RESIDUE SER65 HAS BEEN MUTATED TO GLY. RESIDUES GLY65, TYR66, AND GLY67 CONSTITUTE THE CHROMOPHORE CRO. AUTHOR WOULD LIKE TO KEEP THE CONFLICTS SINCE THEY REPRESENT WHAT GCAMP2 IS. IT IS A MUTAGENESIS STUDY TO OPTIMIZE THE PERFORMACE AGAINST ITS VERY EARLY VERSION IN DATABASE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.01 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 39659 / Observed criterion σ(I): 9.9 / Redundancy: 7.6 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.042

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.453→41.138 Å / SU ML: 0.15 / σ(F): 0.21 / Phase error: 14.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 3171 8.1 %
Rwork0.1321 --
obs0.1356 39139 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.075 Å2 / ksol: 0.396 e/Å3
Refinement stepCycle: LAST / Resolution: 1.453→41.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 0 377 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111907
X-RAY DIFFRACTIONf_angle_d1.4952587
X-RAY DIFFRACTIONf_dihedral_angle_d17.392719
X-RAY DIFFRACTIONf_chiral_restr0.098278
X-RAY DIFFRACTIONf_plane_restr0.007337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.453-1.47480.16481200.07931456X-RAY DIFFRACTION93
1.4748-1.49780.17351200.09141527X-RAY DIFFRACTION96
1.4978-1.52240.19441240.09391526X-RAY DIFFRACTION98
1.5224-1.54860.16661520.09291511X-RAY DIFFRACTION98
1.5486-1.57680.14981360.09181533X-RAY DIFFRACTION98
1.5768-1.60710.17431340.08511544X-RAY DIFFRACTION98
1.6071-1.63990.14961430.08761526X-RAY DIFFRACTION98
1.6399-1.67560.16161470.08251509X-RAY DIFFRACTION98
1.6756-1.71460.16261420.08751565X-RAY DIFFRACTION99
1.7146-1.75740.13991300.08871568X-RAY DIFFRACTION99
1.7574-1.8050.14661230.09191550X-RAY DIFFRACTION99
1.805-1.85810.13781320.09141553X-RAY DIFFRACTION99
1.8581-1.9180.15211240.1011579X-RAY DIFFRACTION99
1.918-1.98660.14771480.09981560X-RAY DIFFRACTION100
1.9866-2.06610.16271510.10511572X-RAY DIFFRACTION100
2.0661-2.16020.18221570.11031563X-RAY DIFFRACTION100
2.1602-2.2740.16691370.11741578X-RAY DIFFRACTION99
2.274-2.41650.19211380.1241592X-RAY DIFFRACTION100
2.4165-2.6030.17051490.13081585X-RAY DIFFRACTION100
2.603-2.86490.19311350.14141611X-RAY DIFFRACTION100
2.8649-3.27940.17071450.13741597X-RAY DIFFRACTION100
3.2794-4.1310.14731380.14071644X-RAY DIFFRACTION100
4.131-41.15480.18981460.18971719X-RAY DIFFRACTION99

+
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