[English] 日本語
Yorodumi
- PDB-3ed8: Application of the superfolder YFP bimolecular fluorescence compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ed8
TitleApplication of the superfolder YFP bimolecular fluorescence complementation for studying protein-protein interactions in vitro
Componentsyellow fluorescence protein
KeywordsLUMINESCENT PROTEIN / superfolder / bimolecular fluorescence complementation
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: 2.7 Å
AuthorsOttmann, C. / Weyand, M.
CitationJournal: Biol.Chem. / Year: 2009
Title: Applicability of superfolder YFP bimolecular fluorescence complementation in vitro.
Authors: Ottmann, C. / Weyand, M. / Wolf, A. / Kuhlmann, J. / Ottmann, C.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 21, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: yellow fluorescence protein
B: yellow fluorescence protein
C: yellow fluorescence protein
D: yellow fluorescence protein
E: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)146,6965
Polymers146,6965
Non-polymers00
Water3,387188
1
A: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.040, 123.040, 247.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
yellow fluorescence protein


Mass: 29339.270 Da / Num. of mol.: 5
Mutation: S30R,Y39I,F64L,F99S,N105K,E111V,I128T,Y145F,M153T,V163A,K166T,I167V,I171V,S205T,A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLY65,TYR66,GLY67 CIRCULARIZED INTO ONE CHROMOPHORE, CRO

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl pH 8.5, 20 % ethanol, 12 % TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9781 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.7→45.98 Å / Num. all: 52991 / Num. obs: 52991 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 61.544 Å2 / Rsym value: 0.111 / Net I/σ(I): 16.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 4.16 / Num. unique all: 5389 / Rsym value: 0.64 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0054refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.084 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21774 2650 5 %RANDOM
Rwork0.17434 ---
obs0.17656 50339 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.262 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8815 0 0 188 9003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.95912332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.76951136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.924.834422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.458151413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0821534
X-RAY DIFFRACTIONr_chiral_restr0.1050.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216981
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5261.55635
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02829063
X-RAY DIFFRACTIONr_scbond_it1.79733445
X-RAY DIFFRACTIONr_scangle_it3.014.53260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 192 -
Rwork0.254 3636 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7826-0.1948-0.26573.1952-0.38161.7937-0.10120.2795-0.0345-0.24280.0764-0.1582-0.0487-0.00310.02480.25950.02190.02840.0299-0.00210.1031-21.320327.6594-25.7692
21.97510.25560.03832.76090.75962.5794-0.2530.07080.3028-0.2263-0.07930.8325-0.0032-0.08340.33240.2109-0.0285-0.13920.012-0.00160.3499-24.9812-2.9256-37.94
34.00340.65380.30423.93721.22552.6931-0.44220.297-0.3124-0.05910.3762-0.10350.1040.89560.0660.2683-0.05370.01740.39980.04940.04911.8853-13.2098-46.0529
42.2575-0.57450.05072.64170.17722.1316-0.2168-0.53770.07980.51190.1551-0.1779-0.202-0.06410.06170.30250.0878-0.08790.16040.02420.1317-13.790420.91152.415
54.61360.26760.36373.2343-0.04042.4240.04660.35010.2478-1.0026-0.1297-0.8381-0.2620.67330.08310.697-0.10270.21590.60960.21730.890533.826217.324-8.7893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 254
2X-RAY DIFFRACTION2B2 - 255
3X-RAY DIFFRACTION3C2 - 255
4X-RAY DIFFRACTION4D2 - 255
5X-RAY DIFFRACTION5E3 - 255

+
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