6B9C | pdb_00006b9c

Superfolder Green Fluorescent Protein with 4-nitro-L-phenylalanine at the chromophore (position 66)

PDB DOI: https://doi.org/10.2210/pdb6B9C/pdb

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

Deposited: 2017-10-10 Released: 2018-10-17
Deposition Author(s): Phillips-Piro, C.M., Brewer, S.H., Olenginski, G.M., Piacentini, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.195 (Depositor), 0.210 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6B9C

This is version 2.1 of the entry. See complete history.

Literature

Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein

Olenginski, G.M., Piacentini, J., Runko, N., Harris, D., Brewer, S.H., Phillips-Piro, C.M.

(2021) Acta Crystallogr D Biol Crystallogr

DOI: https://doi.org/10.1107/S2059798321006525

Macromolecule Content

Total Structure Weight: 26.97 kDa
Atom Count: 2,312
Modeled Residue Count: 234
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	237	Aequorea victoria	Mutation(s): 7 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CQ2 Query on CQ2	A	L-PEPTIDE LINKING	C₁₅ H₁₈ N₄ O₄		GLY, TYR, GLY
GMO Query on GMO	A	L-PEPTIDE LINKING	C₁₅ H₁₆ N₄ O₆		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195 (Depositor), 0.210 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.438	α = 90
b = 55.438	β = 90
c = 165.746	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Phillips-Piro, C.M.

Olenginski, G.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM121984

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2021-08-11
Changes: Advisory, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-12-25
Changes: Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.