4JFG

Crystal structure of sfGFP-66-HqAla

PDB DOI: https://doi.org/10.2210/pdb4JFG/pdb

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

Deposited: 2013-02-28 Released: 2013-10-02
Deposition Author(s): Wang, J., Liu, X., Li, J., Zhang, W., Hu, M., Zhou, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.312
R-Value Work: 0.259
R-Value Observed: 0.262

wwPDB Validation 3D Report Full Report

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

Literature

Significant expansion of the fluorescent protein chromophore through the genetic incorporation of a metal-chelating unnatural amino acid.

Liu, X., Li, J., Hu, C., Zhou, Q., Zhang, W., Hu, M., Zhou, J., Wang, J.

(2013) Angew Chem Int Ed Engl 52: 4805-4809

PubMed: 23554162 Search on PubMed
DOI: https://doi.org/10.1002/anie.201301307
Primary Citation of Related Structures:
4JFG

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: 226.72 kDa
Atom Count: 14,241
Modelled Residue Count: 1,785
Deposited Residue Count: 1,952
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B, C, D, E A, B, C, D, E, F, G, H	244	Aequorea victoria	Mutation(s): 10 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HQY Query on HQY Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain MA [auth G] SDF format, chain P [auth B] SDF format, chain SA [auth H] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D]	DA [auth E] GA [auth F] I [auth A] MA [auth G] P [auth B] DA [auth E], GA [auth F], I [auth A], MA [auth G], P [auth B], SA [auth H], U [auth C], Z [auth D]	quinolin-8-ol C₉ H₇ N O MCJGNVYPOGVAJF-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain SA [auth H] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain SA [auth H] Focus chain U [auth C] Focus chain Z [auth D]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth H] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain UA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain UA [auth H]	AA [auth D] BA [auth D] CA [auth D] EA [auth E] FA [auth E] AA [auth D], BA [auth D], CA [auth D], EA [auth E], FA [auth E], HA [auth F], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], N [auth A], NA [auth G], O [auth A], OA [auth G], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], S [auth B], T [auth B], TA [auth H], UA [auth H], V [auth C], W [auth C], X [auth C], Y [auth C]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KWS Query on KWS	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₉ H₁₃ N₃ O₄		THR, SER, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.312
R-Value Work: 0.259
R-Value Observed: 0.262
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.174	α = 90
b = 148.901	β = 90
c = 161.35	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations