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- PDB-7km4: Crystal Structure of Oxidized Version of Redox-Sensitive Superfol... -

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Basic information

Entry
Database: PDB / ID: 7km4
TitleCrystal Structure of Oxidized Version of Redox-Sensitive Superfolder Green Fluorescent Protein
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Redox Sensitive / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNguyen, T. / Nicely, N.I. / McCafferty, D.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI107951 United States
CitationJournal: To be Published
Title: Crystal Structure of Oxidized Version of Redox-Sensitive Superfolder Green Fluorescent Protein
Authors: Nguyen, T. / Nicely, N.I. / McCafferty, D.G.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)27,8451
Polymers27,8451
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.735, 68.735, 99.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Green fluorescent protein


Mass: 27845.365 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 200, Potassium Chloride, 20% PEG-3350 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 7433 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 56.56 Å2 / Rpim(I) all: 0.031 / Rsym value: 0.059 / Net I/σ(I): 3.3
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 10.3 % / Num. unique obs: 1426 / Rpim(I) all: 0.249 / Rsym value: 0.808 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.65→40.43 Å / SU ML: 0.3792 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.2407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3208 740 10.01 %
Rwork0.2302 6653 -
obs0.2394 7393 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.42 Å2
Refinement stepCycle: LAST / Resolution: 2.65→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 0 9 1769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981798
X-RAY DIFFRACTIONf_angle_d1.27742430
X-RAY DIFFRACTIONf_chiral_restr0.0759266
X-RAY DIFFRACTIONf_plane_restr0.0087315
X-RAY DIFFRACTIONf_dihedral_angle_d18.2027233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.860.35251430.2641283X-RAY DIFFRACTION100
2.86-3.140.4381440.29941302X-RAY DIFFRACTION100
3.14-3.60.38811460.26871311X-RAY DIFFRACTION100
3.6-4.530.32981480.21791330X-RAY DIFFRACTION99.93
4.53-40.430.25041590.19651427X-RAY DIFFRACTION99.94

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