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- PDB-4dkn: Crystal structure of amphioxus green fluorescent protein, GFPA1 -

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Basic information

Entry
Database: PDB / ID: 4dkn
TitleCrystal structure of amphioxus green fluorescent protein, GFPA1
ComponentsAMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE / BETA-CAN / FLUORESCENCE
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: 1.35 Å
AuthorsBomati, E.K. / Deheyn, D.D.
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 1.1Nov 29, 2017Group: Advisory / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_database_related.db_id
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 1.3Dec 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, GFPA1
B: AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1


Theoretical massNumber of molelcules
Total (without water)49,8002
Polymers49,8002
Non-polymers00
Water9,026501
1
A: AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1
B: AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1

A: AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1
B: AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1


Theoretical massNumber of molelcules
Total (without water)99,6004
Polymers99,6004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7720 Å2
ΔGint-22 kcal/mol
Surface area29950 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.254, 125.576, 106.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein AMPHIOXUS GREEN FLUORESCENT PROTEIN, GFPA1


Mass: 24900.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_63256 / Plasmid: PHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3YKQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growpH: 5.5
Details: 100MM CITRIC ACID, 30% PEG 4000, 3% ISOPROPANOL, PH 5.5, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2008
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 84939 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 6.7 %
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GJV

3gjv
PDB Unreleased entry


Resolution: 1.35→32.55 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4172 -RANDOM
Rwork0.192 ---
obs0.192 81943 94 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.589 Å20 Å20 Å2
2---3.449 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.35→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 501 3895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.3712
X-RAY DIFFRACTIONc_scbond_it1.6982
X-RAY DIFFRACTIONc_scangle_it2.4262.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CR2_DIHEDRALS.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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