[English] 日本語
Yorodumi
- PDB-8g0i: High Affinity nanobodies against GFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g0i
TitleHigh Affinity nanobodies against GFP
Components
  • Green fluorescent protein
  • LaG24 Nanobody
KeywordsIMMUNE SYSTEM / Nanobody / nanobodies / GFP / green fluorescent protein / high-affinity antibody variant / antibody variant / single-domain antibody
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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKetaren, N.E. / Rout, M.P. / Almo, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: High Affinity nanobodies against GFP
Authors: Ketaren, N.E. / Rout, M.P. / Almo, S.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
D: LaG24 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6926
Polymers43,5752
Non-polymers1174
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-56 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 86.666, 52.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-319-

HOH

-
Components

#1: Protein Green fluorescent protein /


Mass: 28794.396 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 (E. coli) / References: UniProt: P42212
#2: Antibody LaG24 Nanobody


Mass: 14780.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium chloride, 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0705 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0705 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19251 / % possible obs: 99.5 % / Redundancy: 10 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Χ2: 1.529 / Net I/av σ(I): 33.886 / Net I/σ(I): 23.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 7 / Num. unique obs: 864 / Rsym value: 0.726 / Χ2: 0.835

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.65 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1840 10.03 %
Rwork0.1811 --
obs0.1869 18349 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 4 66 2721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132709
X-RAY DIFFRACTIONf_angle_d1.2793665
X-RAY DIFFRACTIONf_dihedral_angle_d6.671367
X-RAY DIFFRACTIONf_chiral_restr0.059394
X-RAY DIFFRACTIONf_plane_restr0.01479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.32611180.24071055X-RAY DIFFRACTION79
2.26-2.330.26771280.21561125X-RAY DIFFRACTION87
2.33-2.410.3171360.22031200X-RAY DIFFRACTION92
2.41-2.490.30351470.20531217X-RAY DIFFRACTION92
2.49-2.590.25131310.1871237X-RAY DIFFRACTION94
2.59-2.710.24171380.19341280X-RAY DIFFRACTION96
2.71-2.850.25461420.19611256X-RAY DIFFRACTION97
2.85-3.030.25741480.19761306X-RAY DIFFRACTION97
3.03-3.270.25471420.18041329X-RAY DIFFRACTION98
3.27-3.590.22321460.18471335X-RAY DIFFRACTION100
3.59-4.110.24871550.18141340X-RAY DIFFRACTION99
4.11-5.180.19121540.14271368X-RAY DIFFRACTION100
5.18-44.650.24471550.18491461X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.0606 Å / Origin y: 93.5342 Å / Origin z: 62.2825 Å
111213212223313233
T0.391 Å2-0.0066 Å20.0523 Å2-0.379 Å20.0135 Å2--0.4238 Å2
L1.0499 °2-0.0877 °20.5191 °2-0.4235 °20.0381 °2--1.4592 °2
S-0.0242 Å °-0.0034 Å °0.0281 Å °0.0295 Å °-0.022 Å °0.0211 Å °-0.0537 Å °0.0233 Å °-0.0005 Å °
Refinement TLS groupSelection details: all

+
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