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- PDB-3gj1: Non photoactivated state of PA-GFP -

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Basic information

Entry
Database: PDB / ID: 3gj1
TitleNon photoactivated state of PA-GFP
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / beta barrel / Chromophore / Luminescence / Photoprotein
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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHenderson, J.N. / Gepshtein, R. / Heenan, J.R. / Kallio, K. / Huppert, D. / Remington, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structure and mechanism of the photoactivatable green fluorescent protein.
Authors: Henderson, J.N. / Gepshtein, R. / Heenan, J.R. / Kallio, K. / Huppert, D. / Remington, S.J.
History
DepositionMar 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,55814
Polymers103,9014
Non-polymers65810
Water11,097616
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1073
Polymers25,9751
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1424
Polymers25,9751
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1073
Polymers25,9751
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2034
Polymers25,9751
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.515, 86.721, 144.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Green fluorescent protein


Mass: 25975.154 Da / Num. of mol.: 4 / Mutation: Q80R, F99S, M153T, V163A, T203H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M Ammonium sulfate, 0.1 M Tris-HCl, 0.2 M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 91885 / % possible obs: 93.5 % / Observed criterion σ(I): 5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.044 / Χ2: 0.958 / Net I/σ(I): 25.476
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.473 / Num. unique all: 8337 / Χ2: 0.766 / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.549 / Cor.coef. Fo:Fc: 0.283
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EMA

1ema


Resolution: 1.8→46.37 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.81 / SU B: 3.168 / SU ML: 0.099 / SU R Cruickshank DPI: 0.146 / SU Rfree: 0.142 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4596 5 %RANDOM
Rwork0.209 ---
obs0.211 91807 93.33 %-
all-91885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.84 Å2 / Biso mean: 22.938 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7146 0 30 621 7797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0217359
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.9610027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0424.761355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.195151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0121529
X-RAY DIFFRACTIONr_chiral_restr0.1450.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215737
X-RAY DIFFRACTIONr_mcbond_it1.2171.54512
X-RAY DIFFRACTIONr_mcangle_it1.99327283
X-RAY DIFFRACTIONr_scbond_it3.04732847
X-RAY DIFFRACTIONr_scangle_it4.4914.52717
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 268 -
Rwork0.29 5723 -
all-5991 -
obs--83.15 %

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