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- PDB-2qlg: mPlum -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2qlg
TitlemPlum
Components(Fluorescent protein plum) x 2
KeywordsFLUORESCENT PROTEIN / far-red fluorescent protein / acylimine
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShu, X. / Remington, S.J.
CitationJournal: To be Published
Title: Structural Studies of Far-Red Emission in mPlum, a Monomeric Red Fluorescent Protein
Authors: Shu, X. / Wang, L. / Colip, L. / Kallio, K. / Remington, S.J.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 400COMPOUND RELATED TO PROTEIN THE TWO CHAINS IN ASSYMETRIC UNIT HAD THE SAME SEQUENCE EXCEPT AT THE ...COMPOUND RELATED TO PROTEIN THE TWO CHAINS IN ASSYMETRIC UNIT HAD THE SAME SEQUENCE EXCEPT AT THE CHROMPHORE. THE CH6 OF CHAIN A AND NRQ OF CHAIN B BOTH COME FROM THE SAME PARENT RESIDUES MET, TYR AND GLY. AUTHOR STATED THAT THE CA1-N BOND OF CH6 IS SINGLE BOND BUT THE CA1-N OF NRQ IS DOUBLE BOND THAT EXTENDS THE CHROMOPHORE CONJUGATION SYSTEM. THIS IS THE ONLY DIFFERENCE BETWEEN CR2 AND CR3. AUTHOR ALSO STATED THAT CR2 IS A RED FLUORESCENT PROTEIN CHROMOPHORE, WHILE CR3 IS A GREEN FLUORESCENT PROTEIN CHROMOPHORE, DUE TO DIFFERENT CONJUGATION LENGTH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein plum
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)51,2122
Polymers51,2122
Non-polymers00
Water8,791488
1
A: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6071
Polymers25,6071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6051
Polymers25,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.192, 78.276, 96.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fluorescent protein plum


Mass: 25606.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q5S3G7
#2: Protein Fluorescent protein plum


Mass: 25604.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S3G7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growpH: 8.5 / Details: 200mM NaCl, 100mM Tris pH8.5, 30% PEG 3400

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorDate: Sep 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 43227

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Processing

Software
NameClassification
HKL-2000data collection
TNTrefinement
HKL-2000data reduction
HKL-2000data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G7K

1g7k


Resolution: 1.8→10 Å
RfactorNum. reflection
Rfree0.243 -
Rwork0.173 -
all0.173 -
obs0.173 43227
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 0 488 3945

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