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- PDB-2g16: Structure of S65A Y66S GFP variant after backbone fragmentation -

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Basic information

Entry
Database: PDB / ID: 2g16
TitleStructure of S65A Y66S GFP variant after backbone fragmentation
Components(Green fluorescent protein) x 2
KeywordsLUMINESCENT PROTEIN / Beta barrel / chromophore / biosynthesis / fragmentaion / denaturation
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich ...Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBarondeau, D.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Understanding GFP Posttranslational Chemistry: Structures of Designed Variants that Achieve Backbone Fragmentation, Hydrolysis, and Decarboxylation.
Authors: Barondeau, D.P. / Kassmann, C.J. / Tainer, J.A. / Getzoff, E.D.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr2_label_atom_id
Remark 999SEQUENCE Ser 65 in the database has been mutated to alanine, Tyr 66 in the database has been ...SEQUENCE Ser 65 in the database has been mutated to alanine, Tyr 66 in the database has been mutated to serine. Residues Ala 65, Ser 66 and Gly 67 consitute the chromophore CRW 66. This ligand underwent denaturation-induced backbone fragmentation between the C1 and CA1 atoms resulting in fragmented CRW ligand and an E1H molecule

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,7492
Polymers26,7492
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-32 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 62.600, 70.200
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 Green fluorescent protein /


Mass: 6930.946 Da / Num. of mol.: 1 / Fragment: residues 2-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42212
#2: Protein Green fluorescent protein /


Mass: 19818.086 Da / Num. of mol.: 1 / Fragment: residues 65-238 / Mutation: S65A, Y66S, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42212
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM MgCl2, 50 mM Hepes, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.85 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 15928 / Num. obs: 15582 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19 Å2 / Rsym value: 0.075 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.254 / % possible all: 97.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ema

1ema


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 1163 Random
Rwork0.202 --
all-14623 -
obs-13460 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 173 1965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg0.016
LS refinement shellResolution: 2→2.03 Å /
RfactorNum. reflection
Rfree0.333 48
Rwork0.247 -
obs-544

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