4DKM | pdb_00004dkm

Crystal Structure of Amphioxus GFPc1a

PDB DOI: https://doi.org/10.2210/pdb4DKM/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Branchiostoma floridae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-02-03 Released: 2013-05-15
Deposition Author(s): Deheyn, D.D., Bomati, E.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.320 (Depositor), 0.307 (DCC)
R-Value Work:
0.293 (Depositor), 0.297 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4DKM

This is version 1.3 of the entry. See complete history.

Literature

Fluorescent proteins in Amphioxus have strickingly different brightness, yet only few (but key) molecular differences

Bomati, E.K., Haley, J.E., Noel, J.P., Deheyn, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 189.21 kDa
Atom Count: 13,957
Modeled Residue Count: 1,712
Deposited Residue Count: 1,712
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amphioxus Green Fluorescent Protein, GFPc1a	A, B, C, D, E A, B, C, D, E, F, G, H	214	Branchiostoma floridae	Mutation(s): 1 Gene Names: BRAFLDRAFT_75523
UniProt
Find proteins for C3YRA3 (Branchiostoma floridae) Explore C3YRA3 Go to UniProtKB: C3YRA3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3YRA3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.320 (Depositor), 0.307 (DCC)
R-Value Work: 0.293 (Depositor), 0.297 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.76	α = 90
b = 130.46	β = 128.39
c = 106.33	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 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.