[English] 日本語
Yorodumi
- PDB-4pfe: Crystal structure of vsfGFP-0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pfe
TitleCrystal structure of vsfGFP-0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / beta barrel / fusion protein / homodimer / IMMUNE SYSTEM
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 / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsJauch, R. / Chen, S.L.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research FoundationNRF-RF2010-10 Singapore
Agency for Science, Technology, and Research/Genome Institute of Singapore Singapore
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Rational Structure-Based Design of Bright GFP-Based Complexes with Tunable Dimerization.
Authors: Eshaghi, M. / Sun, G. / Gruter, A. / Lim, C.L. / Chee, Y.C. / Jung, G. / Jauch, R. / Wohland, T. / Chen, S.L.
History
DepositionApr 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)77,1222
Polymers77,1222
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-1 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.426, 83.426, 228.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Antibody Green fluorescent protein / vsfGFP-0


Mass: 38561.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: superfolder GFP variant fused Enhancer nanobody
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Vicugna pacos (alpaca)
Gene: GFP / Plasmid: pBAD33 / Cell line (production host): TOP10 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CRO 66.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium acetate pH 4.6 30 %(v/v) PEG 400, 20mM Hepes pH 7.5, 150mM NaCl
PH range: 4.6-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.603→47.16 Å / Num. obs: 25661 / % possible obs: 99.95 % / Redundancy: 32 % / Biso Wilson estimate: 59.24 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.97
Reflection shellResolution: 2.603→2.696 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.9 / % possible all: 99.48

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K1K

3k1k


Resolution: 2.603→47.16 Å / FOM work R set: 0.7791 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1307 5.1 %
Rwork0.1985 24326 -
obs0.2013 25633 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.49 Å2 / Biso mean: 52.98 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 2.603→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 0 141 5555
Biso mean---39.41 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045539
X-RAY DIFFRACTIONf_angle_d1.0457487
X-RAY DIFFRACTIONf_chiral_restr0.065798
X-RAY DIFFRACTIONf_plane_restr0.004981
X-RAY DIFFRACTIONf_dihedral_angle_d16.0922031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6029-2.70710.35681490.272609275899
2.7071-2.83030.34771380.273426502788100
2.8303-2.97950.3691450.277326642809100
2.9795-3.16620.34111560.254526312787100
3.1662-3.41050.27321380.237726682806100
3.4105-3.75360.26991580.199226872845100
3.7536-4.29650.2281590.176126962855100
4.2965-5.41190.1761370.14727572894100
5.4119-47.16860.24381270.188729643091100
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)
12.5267-0.1898-0.14473.89651.8524.28740.2095-0.0650.36330.09220.0819-0.3738-0.6550.3653-0.24060.3603-0.10980.06420.3299-0.02590.346332.2126155.191111.5501
22.7332-0.5255-0.24673.28180.34442.37040.18060.0568-0.1807-0.5354-0.1262-0.12570.27390.1541-0.08880.56820.08550.06540.20780.0760.3284-1.8538141.90635.4768
31.6333-0.86521.14662.8167-1.31862.81070.24290.13990.1991-0.3365-0.3799-0.3201-0.46490.66640.10220.84480.00620.17270.1940.03620.3689-4.686169.614724.6139
41.2923-0.7891-0.06043.2420.69572.25890.085-0.0532-0.15290.3727-0.2720.29470.2313-0.63050.11270.2153-0.05940.02850.6827-0.07930.281612.75135.7950.6192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:229)A2 - 229
2X-RAY DIFFRACTION2(chain A and resid 230:346)A230 - 346
3X-RAY DIFFRACTION3(chain B and resid 3:229)B3 - 229
4X-RAY DIFFRACTION4(chain B and resid 230:345)B230 - 345

+
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