7LSC | pdb_00007lsc

Crystal structure of near-infrared fluorescent protein miRFP670nano3

PDB DOI: https://doi.org/10.2210/pdb7LSC/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-18 Released: 2022-02-23
Deposition Author(s): Pletnev, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.237 (Depositor), 0.265 (DCC)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Near-infrared fluorescent protein with enhanced brightness.

Pletnev, S.

To be published.

Macromolecule Content

Total Structure Weight: 77.69 kDa
Atom Count: 5,492
Modeled Residue Count: 604
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
miRFP670nano3	A, B, C, D	163	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JRA (Subject of Investigation/LOI) Query on JRA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	3-[2-[(~{Z})-[5-[(~{Z})-[(3~{S},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C₃₃ H₃₆ N₄ O₆ WLDQKQLRZDEERT-YTUMONHESA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.237 (Depositor), 0.265 (DCC)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.531	α = 90
b = 73.953	β = 101.71
c = 83.743	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2022-04-13
Changes: Database references
Version 1.2: 2022-04-27
Changes: Database references
Version 1.3: 2023-10-18
Changes: Data collection, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

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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.