[English] 日本語
Yorodumi
- PDB-7e53: Crystal structure of sfGFP complexed with the nanobody nb2 at 2.2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+53
TitleCrystal structure of sfGFP complexed with the nanobody nb2 at 2.2 Angstron resolution
Components
  • Green fluorescent protein's nanobody nb2
  • Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / Aequorea victoria / Camelus bactrianus
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDing, Y. / Zhong, P.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070939 China
National Natural Science Foundation of China (NSFC)82030106 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural insights into two distinct nanobodies recognizing the same epitope of green fluorescent protein.
Authors: Zhong, P. / Wang, Z. / Cheng, S. / Zhang, Y. / Jiang, H. / Liu, R. / Ding, Y.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein's nanobody nb2


Theoretical massNumber of molelcules
Total (without water)40,0832
Polymers40,0832
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.207, 123.991, 108.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Green fluorescent protein /


Mass: 26098.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059PIQ0
#2: Antibody Green fluorescent protein's nanobody nb2


Mass: 13984.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) Polyethylene glycol 400, 100mM CAPS/ Sodium hydroxide, pH 10.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 21347 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.086 / Rrim(I) all: 0.273 / Χ2: 0.958 / Net I/σ(I): 9.8 / Num. measured all: 133097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.10.46719430.340.2120.5171.38589.1
2.28-2.3730.40119570.2540.240.4710.73688.9
2.37-2.483.60.3820910.5270.2090.4380.78594.5
2.48-2.614.60.37220750.6850.1760.4140.86195.9
2.61-2.775.40.34721320.810.1470.3790.90596.8
2.77-2.996.10.3121840.9150.1210.3340.89298.6
2.99-3.296.80.27521860.9350.1020.2940.93798.7
3.29-3.768.50.27322040.9570.0890.2881.07898.7
3.76-4.7390.24722330.9540.080.260.98499
4.73-30100.24623420.9640.0770.2590.91399.4

-
Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P, 6ITQ

2b3p

6itq


Resolution: 2.21→29.81 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 916 5 %
Rwork0.2037 17391 -
obs0.2065 18307 82.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.88 Å2 / Biso mean: 44.0677 Å2 / Biso min: 14.3 Å2
Refinement stepCycle: final / Resolution: 2.21→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 0 92 2875
Biso mean---36.55 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.320.378480.290680685427
2.32-2.470.3623940.28371953204766
2.47-2.660.28181540.27082695284990
2.66-2.930.33751440.25072935307998
2.93-3.350.27961480.21772960310898
3.35-4.220.24211580.18242975313398
4.22-29.810.2051700.1573067323797

+
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