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- PDB-1jc1: CRYSTAL STRUCTURE ANALYSIS OF A REDOX-SENSITIVE GREEN FLUORESCENT... -

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Basic information

Entry
Database: PDB / ID: 1jc1
TitleCRYSTAL STRUCTURE ANALYSIS OF A REDOX-SENSITIVE GREEN FLUORESCENT PROTEIN VARIANT IN A OXIDIZED FORM
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / Beta Barrel / Chromophore / Disulfide Bond
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 / Resolution: 1.9 Å
AuthorsHanson, G.T. / Aggeler, R. / Oglesbee, D. / Cannon, M. / Capaldi, R.A. / Tsien, R.Y. / Remington, S.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators.
Authors: Hanson, G.T. / Aggeler, R. / Oglesbee, D. / Cannon, M. / Capaldi, R.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionJun 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 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 30, 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


Theoretical massNumber of molelcules
Total (without water)80,6593
Polymers80,6593
Non-polymers00
Water3,135174
1
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8861
Polymers26,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8861
Polymers26,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8861
Polymers26,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.838, 67.606, 56.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / Redox Sensitive Green Fluorescent Protein / rosGFP2


Mass: 26886.379 Da / Num. of mol.: 3 / Mutation: C48S,F64L,S65T,Q80R,S147C,Q204C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pRSETb / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Lithium Sulfate, Tris, Copper (II) Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMHEPES1droppH7.9
30.1 MTris1reservoirpH8.5
40.07-0.1 M1reservoirLiSO4
517-22 %PEG40001reservoir
65 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2000
Details: 58 cm long, Pt-coated fused silica, vertical focus mirror
RadiationMonochromator: Cylindrically bent triangular Si(111) asymmetric cut horizontal focus
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→29.7 Å / Num. all: 203865 / Num. obs: 56854 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4181 / % possible all: 100
Reflection
*PLUS
Num. measured all: 203865
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 100 % / Rmerge(I) obs: 0.247

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 1.9→30 Å / Stereochemistry target values: ENGH & HUBER /
RfactorNum. reflection
Rwork0.229 -
obs-56783
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 0 174 5394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg3.111
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_dihedral_angle_d20.113
LS refinement shellResolution: 1.9→1.94 Å
RfactorNum. reflection% reflection
Rwork0.35 --
obs-5602 100 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 54921 / Num. reflection Rfree: 5471 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.317
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.113

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