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

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Basic information

Entry
Database: PDB / ID: 7pcz
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 / ETHANOL / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 4, 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,82511
Polymers53,3642
Non-polymers4619
Water6,269348
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8204
Polymers26,6821
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0047
Polymers26,6821
Non-polymers3226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.110, 68.920, 68.450
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Green fluorescent protein


Mass: 26682.049 Da / Num. of mol.: 2
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-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 10% polyethylenglycol (PEG) 6000, 30% ethanol and 100 mM natriumacetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.35→45.353 Å / Num. obs: 95798 / % possible obs: 94.75 % / Redundancy: 5.1 % / Biso Wilson estimate: 17.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Net I/σ(I): 17.67
Reflection shellResolution: 1.35→1.398 Å / Rmerge(I) obs: 0.3782 / Num. unique obs: 6718 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PCA

7pca


Resolution: 1.35→45.35 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 5747 6 %
Rwork0.1719 --
obs0.1735 95723 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 30 348 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133942
X-RAY DIFFRACTIONf_angle_d1.3215338
X-RAY DIFFRACTIONf_dihedral_angle_d19.3423307
X-RAY DIFFRACTIONf_chiral_restr0.111590
X-RAY DIFFRACTIONf_plane_restr0.01692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.35831210.29811885X-RAY DIFFRACTION60
1.3653-1.38140.28771350.28282111X-RAY DIFFRACTION67
1.3814-1.39830.27191470.26842306X-RAY DIFFRACTION74
1.3983-1.4160.26761610.25782518X-RAY DIFFRACTION79
1.416-1.43460.30321740.24592715X-RAY DIFFRACTION86
1.4346-1.45420.27131840.23372889X-RAY DIFFRACTION91
1.4542-1.4750.21341940.233033X-RAY DIFFRACTION97
1.475-1.4970.26512010.20573158X-RAY DIFFRACTION99
1.497-1.52040.24932000.20493117X-RAY DIFFRACTION100
1.5204-1.54540.20632000.19513130X-RAY DIFFRACTION99
1.5454-1.5720.23981980.18643113X-RAY DIFFRACTION100
1.572-1.60060.21592030.18123176X-RAY DIFFRACTION100
1.6006-1.63140.20612010.17863139X-RAY DIFFRACTION99
1.6314-1.66470.18762000.17683141X-RAY DIFFRACTION100
1.6647-1.70090.23012020.18223159X-RAY DIFFRACTION100
1.7009-1.74040.21251990.18493125X-RAY DIFFRACTION100
1.7404-1.7840.2122020.18433152X-RAY DIFFRACTION99
1.784-1.83220.2212010.18743158X-RAY DIFFRACTION99
1.8322-1.88610.20171990.18513116X-RAY DIFFRACTION99
1.8861-1.9470.19922010.17363145X-RAY DIFFRACTION99
1.947-2.01660.20692020.16753162X-RAY DIFFRACTION99
2.0166-2.09730.18682010.17323146X-RAY DIFFRACTION100
2.0973-2.19280.18492010.16923152X-RAY DIFFRACTION100
2.1928-2.30840.21482030.17713181X-RAY DIFFRACTION100
2.3084-2.4530.21562000.17893143X-RAY DIFFRACTION99
2.453-2.64240.17822020.17093152X-RAY DIFFRACTION99
2.6424-2.90830.19562020.16933165X-RAY DIFFRACTION100
2.9083-3.3290.17972020.16443171X-RAY DIFFRACTION100
3.329-4.19370.19262050.153201X-RAY DIFFRACTION100

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