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- PDB-7dig: Green fluorescent protein from Dendronephthya sp. SSAL-2002 -

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Basic information

Entry
Database: PDB / ID: 7dig
TitleGreen fluorescent protein from Dendronephthya sp. SSAL-2002
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Dendra / Dendronephthya / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / metal ion binding / Green fluorescent protein
Function and homology information
Biological speciesDendronephthya sp. SSAL-2002 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
CitationJournal: Molecules / Year: 2022
Title: Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP.
Authors: Kim, I.J. / Xu, Y. / Nam, K.H.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 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
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein
G: Green fluorescent protein
H: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)206,5798
Polymers206,5798
Non-polymers00
Water00
1
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)103,2894
Polymers103,2894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Green fluorescent protein
F: Green fluorescent protein
G: Green fluorescent protein
H: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)103,2894
Polymers103,2894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.826, 124.737, 129.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Green fluorescent protein


Mass: 25822.318 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendronephthya sp. SSAL-2002 (invertebrata)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8T6U0
Has ligand of interestN
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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: Tris, MgCl2, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 55239 / % possible obs: 95.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2523 / % possible all: 89.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EXB

5exb


Resolution: 2.6→48.7 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 17.242 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 2707 4.9 %RANDOM
Rwork0.2342 ---
obs0.2364 52498 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.33 Å2 / Biso mean: 39.75 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.58 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.6→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14264 0 0 0 14264
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01314656
X-RAY DIFFRACTIONr_bond_other_d0.0040.01713272
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.67419792
X-RAY DIFFRACTIONr_angle_other_deg1.1951.59330952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8751728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23823.263760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.408152512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0381564
X-RAY DIFFRACTIONr_chiral_restr0.0570.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216176
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023064
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 216 -
Rwork0.372 3306 -
all-3522 -
obs--83.68 %

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