8QWJ | pdb_00008qwj

Structure of GFP variant

PDB DOI: https://doi.org/10.2210/pdb8QWJ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-10-19 Released: 2024-12-04
Deposition Author(s): Lenz, M., Fiedler, M., Bellini, D., Chin, J.W.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.278 (Depositor), 0.276 (DCC)
R-Value Work:
0.238 (Depositor), 0.245 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QWJ

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a GFP variant

Lenz, M., Fiedler, M., Bellini, D., Chin, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 28.05 kDa
Atom Count: 1,984
Modeled Residue Count: 227
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	245	Aequorea victoria	Mutation(s): 14 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY
X5U Query on X5U	A	L-PEPTIDE LINKING	C₁₀ H₁₂ I N O₂		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.278 (Depositor), 0.276 (DCC)
R-Value Work: 0.238 (Depositor), 0.245 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.894	α = 90
b = 68.275	β = 90
c = 112.784	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2024-12-04
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.