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 (Depositor), 0.310 (DCC)
R-Value Work:
0.259 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
View more details

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 LOADING

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] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain U [auth C] mmCIF 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 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 UA [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 IA [auth F] 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 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 UA [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 IA [auth F] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain IA [auth F]	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 (Depositor), 0.310 (DCC)
R-Value Work: 0.259 (Depositor), 0.260 (DCC)
R-Value Observed: 0.262 (Depositor)

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