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- PDB-4dkm: Crystal Structure of Amphioxus GFPc1a -

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Basic information

Entry
Database: PDB / ID: 4dkm
TitleCrystal Structure of Amphioxus GFPc1a
ComponentsAmphioxus Green Fluorescent Protein, GFPc1a
KeywordsFLUORESCENT PROTEIN / beta-can / chromophore
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDeheyn, D.D. / Bomati, E.K.
CitationJournal: To be Published
Title: Fluorescent proteins in Amphioxus have strickingly different brightness, yet only few (but key) molecular differences
Authors: Bomati, E.K. / Haley, J.E. / Noel, J.P. / Deheyn, D.D.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 1.2Dec 6, 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: Amphioxus Green Fluorescent Protein, GFPc1a
B: Amphioxus Green Fluorescent Protein, GFPc1a
C: Amphioxus Green Fluorescent Protein, GFPc1a
D: Amphioxus Green Fluorescent Protein, GFPc1a
E: Amphioxus Green Fluorescent Protein, GFPc1a
F: Amphioxus Green Fluorescent Protein, GFPc1a
G: Amphioxus Green Fluorescent Protein, GFPc1a
H: Amphioxus Green Fluorescent Protein, GFPc1a


Theoretical massNumber of molelcules
Total (without water)189,2128
Polymers189,2128
Non-polymers00
Water10,467581
1
A: Amphioxus Green Fluorescent Protein, GFPc1a
B: Amphioxus Green Fluorescent Protein, GFPc1a
F: Amphioxus Green Fluorescent Protein, GFPc1a
G: Amphioxus Green Fluorescent Protein, GFPc1a


Theoretical massNumber of molelcules
Total (without water)94,6064
Polymers94,6064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-25 kcal/mol
Surface area31160 Å2
MethodPISA
2
C: Amphioxus Green Fluorescent Protein, GFPc1a
E: Amphioxus Green Fluorescent Protein, GFPc1a

D: Amphioxus Green Fluorescent Protein, GFPc1a
H: Amphioxus Green Fluorescent Protein, GFPc1a


Theoretical massNumber of molelcules
Total (without water)94,6064
Polymers94,6064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_453-x-1,y,-z-21
Buried area7610 Å2
ΔGint-22 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.760, 130.460, 106.330
Angle α, β, γ (deg.)90.00, 128.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Amphioxus Green Fluorescent Protein, GFPc1a


Mass: 23651.479 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_75523 / Plasmid: T7like / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: C3YRA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 8000, 1M NACL, 100MM HEPES, , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2008
RadiationMonochromator: Double Crystal, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 123007 / Num. obs: 122637 / % possible obs: 99.7 %
Reflection shellResolution: 1.95→2.02 Å / % possible all: 98.2

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G3O

2g3o


Resolution: 1.95→45.02 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3204 5703 Random
Rwork0.2932 --
all-112872 -
obs-103390 -
Refinement stepCycle: LAST / Resolution: 1.95→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13376 0 0 581 13957

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