8DJ8 | pdb_00008dj8

Crystal Structure of Calgreen 1 protein

PDB DOI: https://doi.org/10.2210/pdb8DJ8/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Corynactis californica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-30 Released: 2023-07-05
Deposition Author(s): Hung, L.-W., Nguyen, H.B., Waldo, G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8DJ8

This is version 3.0 of the entry. See complete history.

Literature

Structure and Function of Engineered Variants of GFP-type Green Fluorescent protein from Corynactis californica (tentative)

Nguyen, H.B., Hung, L.-W., Waldo, G.S.

To be published.

Macromolecule Content

Total Structure Weight: 25.1 kDa
Atom Count: 1,871
Modeled Residue Count: 211
Deposited Residue Count: 219
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calgreen One	A	219	Corynactis californica	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
C12 Query on C12	A	L-PEPTIDE LINKING	C₁₅ H₁₈ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.156	α = 90
b = 81.156	β = 90
c = 84.977	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Derived calculations
Version 2.0: 2024-07-10
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-11-13
Changes: Structure summary
Version 3.0: 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.