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- PDB-7cd8: GFP-40/GFPuv complex, Form II -

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Basic information

Entry
Database: PDB / ID: 7cd8
TitleGFP-40/GFPuv complex, Form II
Components
  • GFP-40
  • Green fluorescent protein
KeywordsPROTEIN BINDING / Synthetic binding protein
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYasui, N. / Yamashita, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H05370 Japan
Japan Society for the Promotion of Science (JSPS)19H02841 Japan
CitationJournal: J.Biochem. / Year: 2021
Title: A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins.
Authors: Yasui, N. / Nakamura, K. / Yamashita, A.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
B: Green fluorescent protein
A: GFP-40


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-1 kcal/mol
Surface area15310 Å2
Unit cell
Length a, b, c (Å)51.393, 68.042, 115.892
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: 26811.100 Da / Num. of mol.: 1 / Fragment: UNP residues 3-238 / Mutation: Q80R, F99S, M153T, V163A, A206K
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: Protein GFP-40


Mass: 11554.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5.5% (w/v) PEG 8000, 5% (v/v) ethylene glycol, 50 mM [Co(NH3)6]Cl3, 0.1 M HEPES-Na, pH 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28608 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.998 / Rsym value: 0.074 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1403 / CC1/2: 0.911 / Rsym value: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9C, 2O9U

1b9c

2o9u


Resolution: 2→46.981 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 1389 4.87 %
Rwork0.1718 --
obs0.1741 28550 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 0 298 2936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072712
X-RAY DIFFRACTIONf_angle_d1.0573664
X-RAY DIFFRACTIONf_dihedral_angle_d13.7931003
X-RAY DIFFRACTIONf_chiral_restr0.046382
X-RAY DIFFRACTIONf_plane_restr0.005479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05330.27451090.19522353X-RAY DIFFRACTION87
2.0533-2.13550.22041360.18522718X-RAY DIFFRACTION100
2.1355-2.23270.25221380.18682705X-RAY DIFFRACTION100
2.2327-2.35040.24441420.18732726X-RAY DIFFRACTION100
2.3504-2.49760.27671160.18492717X-RAY DIFFRACTION100
2.4976-2.69040.24381560.18662733X-RAY DIFFRACTION100
2.6904-2.96120.27071390.19112735X-RAY DIFFRACTION100
2.9612-3.38950.20761620.16712746X-RAY DIFFRACTION100
3.3895-4.270.17321480.14782797X-RAY DIFFRACTION100
4.27-5.430.20461430.16452931X-RAY DIFFRACTION100

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