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- PDB-3cb9: Development of a family of redox-sensitive green fluorescent prot... -

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Basic information

Entry
Database: PDB / ID: 3cb9
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: 1.31 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 21, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1853
Polymers28,1371
Non-polymers492
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.066, 62.701, 70.136
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: 28136.545 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M tris, 22% PEG 1550, 0.02M magnesium chloride, pH 8.5, 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: 1.31→50 Å / Num. all: 54553 / Num. obs: 52564 / % possible obs: 99.5 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.31→1.36 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 1.31→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.133 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.052 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16922 2761 5.1 %RANDOM
Rwork0.15212 ---
all0.15341 51740 --
obs0.15299 51740 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 2 309 2154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221900
X-RAY DIFFRACTIONr_bond_other_d0.0010.021274
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9722589
X-RAY DIFFRACTIONr_angle_other_deg0.7853.0013121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22224.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.873158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_nbd_refined0.1870.2265
X-RAY DIFFRACTIONr_nbd_other0.1910.21230
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2869
X-RAY DIFFRACTIONr_nbtor_other0.1120.2999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.51204
X-RAY DIFFRACTIONr_mcbond_other0.2111.5477
X-RAY DIFFRACTIONr_mcangle_it1.1621877
X-RAY DIFFRACTIONr_scbond_it1.5973812
X-RAY DIFFRACTIONr_scangle_it2.2794.5702
X-RAY DIFFRACTIONr_rigid_bond_restr1.33833539
X-RAY DIFFRACTIONr_sphericity_free2.9793304
X-RAY DIFFRACTIONr_sphericity_bonded1.25233124
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 214 -
Rwork0.133 3739 -
obs-3739 98.75 %

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