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- PDB-3cd1: Development of a family of redox-sensitive green fluorescent prot... -

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Basic information

Entry
Database: PDB / ID: 3cd1
TitleDevelopment of a family of redox-sensitive green fluorescent protein indicators for use in relatively oxidizing subcellular environments
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / GFP / redox
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: 1.312 Å
AuthorsLohman, J.R.
CitationJournal: Biochemistry / Year: 2008
Title: Development of a family of redox-sensitive green fluorescent protein indicators for use in relatively oxidizing subcellular environments
Authors: Lohman, J.R. / Remington, S.J.
History
DepositionFeb 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,1391
Polymers28,1391
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.187, 62.363, 68.803
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 / roGFP1-iE / GFP


Mass: 28138.557 Da / Num. of mol.: 1
Mutation: C48S,F64L,F99S,S147CR,H148S,M153T,V163A,I167T,Q204C
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): DH5 alpha / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M tris, 24% PEG 1550, 0.04M sodium acetate, pH 8.0, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 11, 2007
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.312→50 Å / Num. all: 52564 / Num. obs: 52564 / % possible obs: 98.6 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.312→1.36 Å / % possible all: 92.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.312→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.619 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.057 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18377 2655 5.1 %RANDOM
Rwork0.16362 ---
all0.16464 49838 --
obs0.16464 49838 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.312→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 0 263 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221886
X-RAY DIFFRACTIONr_bond_other_d0.0030.021265
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9712564
X-RAY DIFFRACTIONr_angle_other_deg0.7873.0013104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47125.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.986157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02376
X-RAY DIFFRACTIONr_nbd_refined0.2040.2266
X-RAY DIFFRACTIONr_nbd_other0.1930.21227
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2870
X-RAY DIFFRACTIONr_nbtor_other0.1120.2988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0860.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8411.51184
X-RAY DIFFRACTIONr_mcbond_other0.2671.5473
X-RAY DIFFRACTIONr_mcangle_it1.29821858
X-RAY DIFFRACTIONr_scbond_it1.7513801
X-RAY DIFFRACTIONr_scangle_it2.5484.5696
X-RAY DIFFRACTIONr_rigid_bond_restr1.59733502
X-RAY DIFFRACTIONr_sphericity_free3.4743263
X-RAY DIFFRACTIONr_sphericity_bonded1.60833099
LS refinement shellResolution: 1.312→1.346 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 170 -
Rwork0.236 3275 -
obs--88.08 %

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