4GES | pdb_00004ges

crystal structure of GFP-TYR151PYZ with an unnatural amino acid incorporation

PDB DOI: https://doi.org/10.2210/pdb4GES/pdb

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

Deposited: 2012-08-02 Released: 2012-08-29
Deposition Author(s): Dong, J., Liu, X., Li, J., Wang, J., Gong, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free:
0.188 (Depositor), 0.194 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4GES

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

Literature

Genetic incorporation of a metal-chelating amino Acid as a probe for protein electron transfer.

Liu, X., Li, J., Dong, J., Hu, C., Gong, W., Wang, J.

(2012) Angew Chem Int Ed Engl 51: 10261-10265

PubMed: 22936654 Search on PubMed
DOI: https://doi.org/10.1002/anie.201204962
Primary Citation Related Structures:
4GES, 4GF6

Organizational Affiliation

Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 27.88 kDa
Atom Count: 2,070
Modeled Residue Count: 230
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A [auth B]	246	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

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0WZ Query on 0WZ	A [auth B]	L-PEPTIDE LINKING	C₁₂ H₁₃ N₃ O₃		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.188 (Depositor), 0.194 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.717	α = 90
b = 50.809	β = 90
c = 62.364	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2012-10-24
Changes: Database references
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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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.