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- PDB-7cd7: GFP-40/GFPuv complex, Form I -

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Basic information

Entry
Database: PDB / ID: 7cd7
TitleGFP-40/GFPuv complex, Form I
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: 1.704 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 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
B: Green fluorescent protein
D: Green fluorescent protein
A: GFP-40
C: GFP-40


Theoretical massNumber of molelcules
Total (without water)76,7304
Polymers76,7304
Non-polymers00
Water15,529862
1
B: Green fluorescent protein
A: GFP-40


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Green fluorescent protein
C: GFP-40


Theoretical massNumber of molelcules
Total (without water)38,3652
Polymers38,3652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.712, 103.168, 67.861
Angle α, β, γ (deg.)90.00, 106.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein


Mass: 26811.100 Da / Num. of mol.: 2 / 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.: 2
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.: 862 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% (w/v) PEG 4000, 200 mM MgCl2, 0.1 M Tris-HCl, pH 8.5

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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: 1.7→50 Å / Num. obs: 78215 / % possible obs: 99.5 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rsym value: 0.066 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3848 / CC1/2: 0.838 / Rsym value: 0.371

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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: 1.704→47.982 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 3863 4.94 %
Rwork0.1823 --
obs0.1846 78166 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.704→47.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5379 0 0 862 6241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145558
X-RAY DIFFRACTIONf_angle_d1.2987513
X-RAY DIFFRACTIONf_dihedral_angle_d13.2332059
X-RAY DIFFRACTIONf_chiral_restr0.062781
X-RAY DIFFRACTIONf_plane_restr0.007981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.704-1.72470.30031100.24782405X-RAY DIFFRACTION90
1.7247-1.74650.27721310.22742665X-RAY DIFFRACTION100
1.7465-1.76950.29781350.22232697X-RAY DIFFRACTION100
1.7695-1.79370.29911490.21452613X-RAY DIFFRACTION100
1.7937-1.81940.28141400.21412682X-RAY DIFFRACTION100
1.8194-1.84650.26461480.2122638X-RAY DIFFRACTION100
1.8465-1.87540.27031440.21512668X-RAY DIFFRACTION100
1.8754-1.90610.25661360.21292668X-RAY DIFFRACTION100
1.9061-1.9390.26621340.20632646X-RAY DIFFRACTION100
1.939-1.97430.25361390.20572661X-RAY DIFFRACTION100
1.9743-2.01220.2771280.20692697X-RAY DIFFRACTION100
2.0122-2.05330.22161580.1962648X-RAY DIFFRACTION100
2.0533-2.0980.22431530.18932631X-RAY DIFFRACTION100
2.098-2.14680.24711310.19112641X-RAY DIFFRACTION100
2.1468-2.20040.26051310.192708X-RAY DIFFRACTION100
2.2004-2.25990.23741380.18922651X-RAY DIFFRACTION99
2.2599-2.32640.22521300.18262653X-RAY DIFFRACTION99
2.3264-2.40150.27991400.18922659X-RAY DIFFRACTION99
2.4015-2.48740.22951330.18262683X-RAY DIFFRACTION99
2.4874-2.58690.27431390.19012651X-RAY DIFFRACTION100
2.5869-2.70470.22911230.19252677X-RAY DIFFRACTION100
2.7047-2.84720.22391440.19982672X-RAY DIFFRACTION100
2.8472-3.02560.2511320.18582670X-RAY DIFFRACTION100
3.0256-3.25920.221480.17312660X-RAY DIFFRACTION99
3.2592-3.58710.20011330.16792651X-RAY DIFFRACTION99
3.5871-4.10590.18551500.15732647X-RAY DIFFRACTION98
4.1059-5.1720.17891400.14872664X-RAY DIFFRACTION99
5.172-5.430.20841460.17842697X-RAY DIFFRACTION99

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