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- PDB-2a46: Crystal structures of amFP486, a cyan fluorescent protein from An... -

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Basic information

Entry
Database: PDB / ID: 2a46
TitleCrystal structures of amFP486, a cyan fluorescent protein from Anemonia majano, and variants
ComponentsGFP-like fluorescent chromoprotein amFP486
KeywordsLUMINESCENT PROTEIN / Beta Barrel
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
BETA-MERCAPTOETHANOL / GFP-like fluorescent chromoprotein amFP486
Similarity search - Component
Biological speciesAnemonia majano (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHenderson, J.N. / Remington, S.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structures and mutational analysis of amFP486, a cyan fluorescent protein from Anemonia majano
Authors: Henderson, J.N. / Remington, S.J.
History
DepositionJun 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Aug 23, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein amFP486
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6792
Polymers26,6011
Non-polymers781
Water2,630146
1
A: GFP-like fluorescent chromoprotein amFP486
hetero molecules

A: GFP-like fluorescent chromoprotein amFP486
hetero molecules

A: GFP-like fluorescent chromoprotein amFP486
hetero molecules

A: GFP-like fluorescent chromoprotein amFP486
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7178
Polymers106,4044
Non-polymers3134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_575-x,-y+2,z1
crystal symmetry operation15_466y-1,x+1,-z+11
Unit cell
Length a, b, c (Å)112.541, 112.541, 81.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

DetailsThe biological tetramer is generated by the following operations: -y,-x,-z 1-x,1-y,1+z 1+y,1+x,1-z

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Components

#1: Protein GFP-like fluorescent chromoprotein amFP486


Mass: 26600.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia majano (sea anemone) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 DE3 / References: UniProt: Q9U6Y6
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.3
Details: 1 M Sodium/Potassium Tartrate, 0.16 M Lithium Sulfate, 0.1 M CHES pH 9.3, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.82653 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.65→21.7 Å / Num. all: 31872 / Num. obs: 31584 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.064 / Χ2: 0.797
Reflection shellResolution: 1.65→1.71 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.34 / Num. measured obs: 3095 / Χ2: 0.495 / % possible all: 99.5

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Phasing

Phasing MRRfactor: 0.601 / Cor.coef. Fo:Fc: 0.21
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
TNTrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G7K

1g7k


Resolution: 1.65→21.7 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.208 -random
Rwork0.165 --
obs0.167 31572 -
Solvent computationBsol: 150 Å2 / ksol: 0.8 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.65→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 4 146 1857
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.65-1.740.23X-RAY DIFFRACTION280
1.74-1.810.25X-RAY DIFFRACTION310
1.81-1.90.23X-RAY DIFFRACTION270
1.9-20.23X-RAY DIFFRACTION314
2-2.140.22X-RAY DIFFRACTION310
2.14-2.310.22X-RAY DIFFRACTION285
2.31-2.570.2X-RAY DIFFRACTION301
2.57-2.990.21X-RAY DIFFRACTION325
2.99-4.010.21X-RAY DIFFRACTION331
4.01-60.19X-RAY DIFFRACTION332

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