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- PDB-2qli: mPlum E16Q mutant -

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Basic information

Entry
Database: PDB / ID: 2qli
TitlemPlum E16Q mutant
ComponentsFluorescent protein plum
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 / SYNCHROTRON / AB INITIO / Resolution: 1.34 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 1.2Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_validate_polymer_linkage / software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)51,2082
Polymers51,2082
Non-polymers00
Water8,647480
1
A: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6041
Polymers25,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)25,6041
Polymers25,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.164, 77.904, 96.171
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: 25603.928 Da / Num. of mol.: 2 / Mutation: E17Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.03 Å3/Da / Density % sol: 44.77 %
Crystal growpH: 8.5 / Details: 200mM NaCl, 100mM Tris pH8.5, 30% PEG 3400

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 95462

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Processing

Software
NameClassification
SHELXL-97refinement
TNTrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
HKL-2000data collection
RefinementMethod to determine structure: AB INITIO
Starting model: PDB entry 1G7K

1g7k


Resolution: 1.34→10 Å / Num. parameters: 35589 / Num. restraintsaints: 43309 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 4777 5.3 %RANDOM
Rwork0.1834 ---
all0.1834 90685 --
obs0.1834 69658 87.8 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3935
Refinement stepCycle: LAST / Resolution: 1.34→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 0 480 3951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.102

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