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- PDB-2a47: Crystal structure of amFP486 H199T -

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Basic information

Entry
Database: PDB / ID: 2a47
TitleCrystal structure of amFP486 H199T
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: 1.72 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,6422
Polymers26,5641
Non-polymers781
Water2,378132
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)106,5688
Polymers106,2564
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)112.955, 112.955, 81.951
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-417-

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: 26563.953 Da / Num. of mol.: 1 / Mutation: H199T
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.: 132 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.7
Details: 0.6 M Na/K tartrate, 40 M Li2SO4, 0.1 M CHES pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1.72→22.3 Å / Num. all: 27856 / Num. obs: 28008 / % possible obs: 95.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.054 / Χ2: 1.192
Reflection shellResolution: 1.72→1.78 Å / % possible obs: 97.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.383 / Num. measured obs: 2724 / Χ2: 0.499 / % possible all: 97.7

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Phasing

Phasing MRRfactor: 0.27 / Cor.coef. Fo:Fc: 0.818
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
TNTrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A46

2a46


Resolution: 1.72→22.3 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 --random
Rwork0.169 ---
obs0.172 28008 96 %-
Solvent computationBsol: 150 Å2 / ksol: 0.8 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.72→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 4 132 1871

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