2QU1 | pdb_00002qu1

Crystal Structure of a Cyclized GFP Variant

PDB DOI: https://doi.org/10.2210/pdb2QU1/pdb

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

Deposited: 2007-08-03 Released: 2007-09-11
Deposition Author(s): Bailey, L.J., McCoy, J.G., Bitto, E., Bingman, C.A., Fox, B.G., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.168 (Depositor), 0.172 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2QU1

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

Literature

Crystal Structure of a Cyclized GFP Variant.

Bailey, L.J., McCoy, J.G., Bitto, E., Bingman, C.A., Fox, B.G., Wesenberg, G.E., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 27.29 kDa
Atom Count: 2,293
Modeled Residue Count: 232
Deposited Residue Count: 239
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	239	Aequorea victoria	Mutation(s): 5 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
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.220 (Depositor), 0.224 (DCC)
R-Value Work: 0.168 (Depositor), 0.172 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.46	α = 90
b = 61.99	β = 90
c = 70.02	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Wesenberg, G.E.

Phillips Jr., G.N.

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-10-30
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.