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- PDB-7pca: Functional and structural characterization of redox sensitive sup... -

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Basic information

Entry
Database: PDB / ID: 7pca
TitleFunctional and structural characterization of redox sensitive superfolder green fluorescent protein and variants
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / genetically encoded biosensors / x-ray crystal structure / dynamic simulation / redox regulation / Plasmodium falciparum
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / FORMAMIDE / ETHANOL / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsFritz-Wolf, K. / Heimsch, K.C. / Schuh, A.K. / Becker, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
Hessian Ministry of Science, Higher Education and Art (HMWK)Loewe Druid E3 Germany
CitationJournal: Antioxid.Redox Signal. / Year: 2022
Title: Structure and Function of Redox-Sensitive Superfolder Green Fluorescent Protein Variant.
Authors: Heimsch, K.C. / Gertzen, C.G.W. / Schuh, A.K. / Nietzel, T. / Rahlfs, S. / Przyborski, J.M. / Gohlke, H. / Schwarzlander, M. / Becker, K. / Fritz-Wolf, K.
History
DepositionAug 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)27,1197
Polymers26,7521
Non-polymers3666
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint4 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.870, 47.370, 117.740
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: 26752.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli M15 (bacteria) / References: UniProt: P42212
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 46% ETOH, 0.25% v/v Dichloromethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→19.85 Å / Num. obs: 89058 / % possible obs: 91.69 % / Redundancy: 4.4 % / Biso Wilson estimate: 8.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04413 / Rpim(I) all: 0.0227 / Net I/σ(I): 16.24
Reflection shellResolution: 1.05→1.088 Å / Redundancy: 2.1 % / Num. unique obs: 4957 / CC1/2: 0.886 / % possible all: 51.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qyo

1qyo


Resolution: 1.05→19.85 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1625 5351 6 %
Rwork0.1492 --
obs0.15 89190 91.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 24 281 2126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111926
X-RAY DIFFRACTIONf_angle_d1.2162612
X-RAY DIFFRACTIONf_dihedral_angle_d12.911712
X-RAY DIFFRACTIONf_chiral_restr0.096290
X-RAY DIFFRACTIONf_plane_restr0.009339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.3936600.304944X-RAY DIFFRACTION31
1.06-1.070.33811060.25351649X-RAY DIFFRACTION54
1.07-1.080.21041140.21451786X-RAY DIFFRACTION59
1.08-1.10.25441240.24941951X-RAY DIFFRACTION65
1.1-1.110.19771460.18312279X-RAY DIFFRACTION74
1.11-1.130.18781670.18072627X-RAY DIFFRACTION87
1.13-1.140.18191810.17272835X-RAY DIFFRACTION94
1.14-1.160.17311870.16612925X-RAY DIFFRACTION97
1.16-1.180.1751900.16462973X-RAY DIFFRACTION97
1.18-1.20.17521890.16242963X-RAY DIFFRACTION97
1.2-1.220.16551890.16052971X-RAY DIFFRACTION98
1.22-1.240.18151900.16022970X-RAY DIFFRACTION98
1.24-1.270.16761900.1532975X-RAY DIFFRACTION98
1.27-1.290.16691910.15082987X-RAY DIFFRACTION99
1.29-1.320.15851900.15212980X-RAY DIFFRACTION97
1.32-1.350.15811930.1533026X-RAY DIFFRACTION99
1.35-1.380.1621900.15232984X-RAY DIFFRACTION98
1.38-1.420.16141930.15013015X-RAY DIFFRACTION98
1.42-1.460.15681940.15763040X-RAY DIFFRACTION99
1.46-1.510.17751920.14433016X-RAY DIFFRACTION99
1.51-1.560.16991930.14083025X-RAY DIFFRACTION99
1.56-1.630.16981940.13813037X-RAY DIFFRACTION99
1.63-1.70.13921940.14213045X-RAY DIFFRACTION99
1.7-1.790.16351940.13773043X-RAY DIFFRACTION99
1.79-1.90.16441960.13823070X-RAY DIFFRACTION99
1.9-2.050.14051980.12793104X-RAY DIFFRACTION100
2.05-2.260.1341970.13013090X-RAY DIFFRACTION100
2.26-2.580.18051970.14013081X-RAY DIFFRACTION99
2.58-3.250.15422020.14763160X-RAY DIFFRACTION99
3.25-19.850.15322100.15333288X-RAY DIFFRACTION99

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