5NI3 | pdb_00005ni3

sfGFP 204-204 mutant dimer

PDB DOI: https://doi.org/10.2210/pdb5NI3/pdb

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

Deposited: 2017-03-23 Released: 2018-09-12
Deposition Author(s): Worthy, H.L., Rizkallah, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.191 (Depositor), 0.205 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Association of Fluorescent Protein Pairs and Its Significant Impact on Fluorescence and Energy Transfer

Pope, J.R., Johnson, R.L., Jamieson, W.D., Worthy, H.L., Kailasam, S., Ahmed, R.D., Taban, I., Auhim, H.S., Watkins, D.W., Rizkallah, P.J., Castell, O.K., Jones, D.D.

(2020) Adv Sci (Weinh)

DOI: https://doi.org/10.1002/advs.202003167

Macromolecule Content

Total Structure Weight: 104.49 kDa
Atom Count: 8,346
Modeled Residue Count: 908
Deposited Residue Count: 912
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	225	Aequorea victoria	Mutation(s): 2 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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	B	229	Aequorea victoria	Mutation(s): 2 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

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	C, D	229	Aequorea victoria	Mutation(s): 1 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DB5 Query on DB5 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	[(4~{S})-4,5,6,7,8,9-hexahydro-1~{H}-cycloocta[d][1,2,3]triazol-4-yl] hydrogen carbonate C₉ H₁₃ N₃ O₃ ZBJGIWFCJONVKZ-ZETCQYMHSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] SDF format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] MOL2 format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D] mmCIF format, chain J [auth B]	H [auth B], I [auth B], J [auth B], M [auth C], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] K [auth B] N [auth C] O [auth C] E [auth A], F [auth A], K [auth B], N [auth C], O [auth C], P [auth C], S [auth D], T [auth D], U [auth D], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

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: 1.28 Å
R-Value Free: 0.191 (Depositor), 0.205 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.7	α = 90
b = 98.02	β = 90
c = 102.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-09-12

Deposition Author(s):

Worthy, H.L.

Rizkallah, P.J.

Revision History (Full details and data files)

Version 1.0: 2018-09-12
Type: Initial release
Version 1.1: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2019-07-10
Changes: Data collection
Version 1.3: 2019-10-16
Changes: Data collection
Version 1.4: 2020-03-25
Changes: Database references
Version 1.5: 2020-12-02
Changes: Database references, Derived calculations
Version 1.6: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.7: 2024-11-20
Changes: Structure summary

5NI3 | pdb_00005ni3

sfGFP 204-204 mutant dimer

Literature

Association of Fluorescent Protein Pairs and Its Significant Impact on Fluorescence and Energy Transfer

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)