2HJO | pdb_00002hjo

Crystal structure of V224H design intermediate for GFP metal ion reporter

PDB DOI: https://doi.org/10.2210/pdb2HJO/pdb

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

Deposited: 2006-06-30 Released: 2008-04-08
Deposition Author(s): Barondeau, D.P., Tubbs, J.L., Tainer, J.A., Getzoff, E.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.165 (Depositor), 0.164 (DCC)
R-Value Work:
0.128 (Depositor), 0.151 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2HJO

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

Literature

Iterative Structure-Based Design of a Green Fluorescent Protein Metal Ion Reporter

Barondeau, D.P., Tubbs, J.L., Tainer, J.A., Getzoff, E.D.

To be published.

Macromolecule Content

Total Structure Weight: 27.01 kDa
Atom Count: 2,119
Modeled Residue Count: 224
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green Fluorescent Protein	A	236	Aequorea victoria	Mutation(s): 3 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 1.25 Å
R-Value Free: 0.165 (Depositor), 0.164 (DCC)
R-Value Work: 0.128 (Depositor), 0.151 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.63	α = 90
b = 62.15	β = 90
c = 69.136	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Barondeau, D.P.

Revision History (Full details and data files)

Version 1.0: 2008-04-08
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: 2024-11-13
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.