8DPD | pdb_00008dpd

superfolder GFP Tyr74pCNPhe mutant

PDB DOI: https://doi.org/10.2210/pdb8DPD/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-07-15 Released: 2022-08-31
Deposition Author(s): Phillips-Piro, C.M., Papoutsis, B., Piacentini, J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.252 (Depositor), 0.249 (DCC)
R-Value Work:
0.208 (Depositor), 0.205 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DPD

This is version 2.0 of the entry. See complete history.

Literature

Superfolder GFP Tyr74pCNPhe mutant

Phillips-Piro, C.M., Papoutsis, B., Piacentini, J.

To be published.

Macromolecule Content

Total Structure Weight: 27.4 kDa
Atom Count: 2,177
Modeled Residue Count: 228
Deposited Residue Count: 237
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superfolder green fluorescent protein	A	237	Aequorea victoria	Mutation(s): 13 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

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CO2 Query on CO2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4CF Query on 4CF	A	L-PEPTIDE LINKING	C₁₀ H₁₀ N₂ O₂		PHE
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free: 0.252 (Depositor), 0.249 (DCC)
R-Value Work: 0.208 (Depositor), 0.205 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.222	α = 90
b = 47.222	β = 90
c = 346.153	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-31

Deposition Author(s):

Phillips-Piro, C.M.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1847937

Revision History (Full details and data files)

Version 1.0: 2022-08-31
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-11-13
Changes: Structure summary
Version 2.0: 2026-03-18
Changes: Polymer sequence

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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.