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- PDB-7pd0: Functional and structural characterization of redox sensitive sup... -

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Basic information

Entry
Database: PDB / ID: 7pd0
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 16, 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

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,49015
Polymers107,2054
Non-polymers1,28511
Water9,386521
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2084
Polymers26,8011
Non-polymers4063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0133
Polymers26,8011
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2705
Polymers26,8011
Non-polymers4694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9993
Polymers26,8011
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.850, 51.290, 101.460
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Green fluorescent protein


Mass: 26801.236 Da / Num. of mol.: 4
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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 30% PEG 4000.

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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 EIGER2 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: 2→47.92 Å / Num. obs: 59713 / % possible obs: 94.53 % / Redundancy: 2.4 % / CC1/2: 0.991 / Net I/σ(I): 6.76
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 15047 / CC1/2: 0.962

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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: 2→47.919 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2979 3571 6 %
Rwork0.2497 --
obs0.2525 59509 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 85 521 7999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027650
X-RAY DIFFRACTIONf_angle_d0.57210310
X-RAY DIFFRACTIONf_dihedral_angle_d16.6888135
X-RAY DIFFRACTIONf_chiral_restr0.0441121
X-RAY DIFFRACTIONf_plane_restr0.0031326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02630.30371350.24372121X-RAY DIFFRACTION93
2.0263-2.05410.27951320.25712076X-RAY DIFFRACTION93
2.0541-2.08340.29981330.25032086X-RAY DIFFRACTION94
2.0834-2.11450.28851360.25992140X-RAY DIFFRACTION93
2.1145-2.14760.30991350.26192113X-RAY DIFFRACTION93
2.1476-2.18280.31061350.26712113X-RAY DIFFRACTION94
2.1828-2.22040.34861360.26212124X-RAY DIFFRACTION94
2.2204-2.26080.3361350.27962104X-RAY DIFFRACTION95
2.2608-2.30430.3451350.26582127X-RAY DIFFRACTION93
2.3043-2.35130.24991350.26012115X-RAY DIFFRACTION93
2.3513-2.40240.2781340.25822092X-RAY DIFFRACTION93
2.4024-2.45830.31391370.26522153X-RAY DIFFRACTION94
2.4583-2.51980.29751360.25582144X-RAY DIFFRACTION95
2.5198-2.58790.29361390.25862174X-RAY DIFFRACTION96
2.5879-2.66410.30021370.2632162X-RAY DIFFRACTION96
2.6641-2.750.34811410.28092209X-RAY DIFFRACTION97
2.75-2.84830.31661400.29732200X-RAY DIFFRACTION96
2.8483-2.96230.31251370.28982140X-RAY DIFFRACTION96
2.9623-3.09710.2761410.26452201X-RAY DIFFRACTION96
3.0971-3.26040.3381390.2612185X-RAY DIFFRACTION95
3.2604-3.46460.30091390.25042159X-RAY DIFFRACTION95
3.4646-3.7320.31941420.24332223X-RAY DIFFRACTION97
3.732-4.10740.28571400.22642192X-RAY DIFFRACTION96
4.1074-4.70130.25231420.22231X-RAY DIFFRACTION96
4.7013-5.92140.29051400.22592184X-RAY DIFFRACTION95
5.9214-47.910.27651400.24922170X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 18.6988 Å / Origin y: -16.0714 Å / Origin z: 22.016 Å
111213212223313233
T0.1792 Å2-0.0144 Å2-0.0054 Å2-0.1754 Å2-0.0243 Å2--0.2418 Å2
L0.1535 °2-0.0445 °2-0.0344 °2-0.1159 °20.0625 °2--0.5019 °2
S-0.0078 Å °-0.0024 Å °0.0279 Å °0.0045 Å °-0.0161 Å °0.0115 Å °0.0305 Å °-0.1022 Å °0.0188 Å °
Refinement TLS groupSelection details: all

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