4NQG | pdb_00004nqg

Crystal Structure of Ca(2+)-regulated photoprotein mitrocomin from Jellyfish Mitrocoma cellularia at 1.3 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4NQG/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Mitrocoma cellularia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-25 Released: 2014-11-26
Deposition Author(s): Natashin, P.V., Vysotski, E.S., Liu, Z.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.161 (Depositor), 0.167 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Multiple Isospecies of Ca(2+)-regulated Photoprotein Mitrocomin from Jellyfish Mitrocoma cellularia: Cloning, Characterization, and Crystal Structure

Burakova, L.P., Natashin, P.V., Markova, S.V., Eremeeva, E.V., Shimomura, O., Liu, Z.J., Vysotski, E.S.

To be published.

Macromolecule Content

Total Structure Weight: 46.06 kDa
Atom Count: 3,783
Modeled Residue Count: 394
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitrocomin	A, B	197	Mitrocoma cellularia	Mutation(s): 0 Gene Names: MI17
UniProt
Find proteins for P39047 (Mitrocoma cellularia) Explore P39047 Go to UniProtKB: P39047
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39047
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CZH Query on CZH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	C2-HYDROPEROXY-COELENTERAZINE C₂₆ H₂₁ N₃ O₅ HOSWCJDTHOAORT-SANMLTNESA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.161 (Depositor), 0.167 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.898	α = 90
b = 69.682	β = 90.03
c = 49.929	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.