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- PDB-7dna: Photocleavable Fluorescent Protein in green and red form -

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Basic information

Entry
Database: PDB / ID: 7dna
TitlePhotocleavable Fluorescent Protein in green and red form
Components(Green-to-red photoconvertible GFP-like protein) x 3
KeywordsFLUORESCENT PROTEIN / PhoCl / Green form / Photocleavable
Function / homologyAMINO GROUP
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWen, Y. / Lemieux, J.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870132 China
CitationJournal: Chem Sci / Year: 2021
Title: Photocleavable proteins that undergo fast and efficient dissociation.
Authors: Lu, X. / Wen, Y. / Zhang, S. / Zhang, W. / Chen, Y. / Shen, Y. / Lemieux, M.J. / Campbell, R.E.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / database_PDB_caveat / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.Z_PDB / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_seq_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 4.0Sep 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.end_label_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green-to-red photoconvertible GFP-like protein
B: Green-to-red photoconvertible GFP-like protein
D: Green-to-red photoconvertible GFP-like protein
F: Green-to-red photoconvertible GFP-like protein
J: Green-to-red photoconvertible GFP-like protein
I: Green-to-red photoconvertible GFP-like protein
L: Green-to-red photoconvertible GFP-like protein
K: Green-to-red photoconvertible GFP-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,36610
Polymers165,3348
Non-polymers322
Water6,287349
1
A: Green-to-red photoconvertible GFP-like protein


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9800 Å2
MethodPISA
2
B: Green-to-red photoconvertible GFP-like protein


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9800 Å2
MethodPISA
3
D: Green-to-red photoconvertible GFP-like protein


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9590 Å2
MethodPISA
4
F: Green-to-red photoconvertible GFP-like protein
J: Green-to-red photoconvertible GFP-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6723
Polymers27,6562
Non-polymers161
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12 kcal/mol
Surface area9740 Å2
MethodPISA
5
I: Green-to-red photoconvertible GFP-like protein
L: Green-to-red photoconvertible GFP-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6723
Polymers27,6562
Non-polymers161
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area9750 Å2
MethodPISA
6
K: Green-to-red photoconvertible GFP-like protein


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.930, 72.490, 126.550
Angle α, β, γ (deg.)92.460, 97.310, 92.500
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Green-to-red photoconvertible GFP-like protein


Mass: 27505.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: chromophore CR8 included / Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#2: Protein Green-to-red photoconvertible GFP-like protein


Mass: 26150.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chromophore IEY included, When the protein is photo-cleaved CR8 turns into IEY and the N turns into NFA.
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Green-to-red photoconvertible GFP-like protein


Mass: 1505.700 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chromophore IEY included, When the protein is photo-cleaved CR8 turns into IEY and the N turns into NFA.
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB buffer pH 6.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→46.27 Å / Num. obs: 58440 / % possible obs: 95.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 9388 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQK

2hqk


Resolution: 2.3→46.27 Å / SU ML: 0.3159 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.0625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 1991 4.28 %
Rwork0.2211 44577 -
obs0.2232 46568 76.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.85 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10137 0 172 349 10658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004510590
X-RAY DIFFRACTIONf_angle_d0.863314252
X-RAY DIFFRACTIONf_chiral_restr0.05171452
X-RAY DIFFRACTIONf_plane_restr0.00481829
X-RAY DIFFRACTIONf_dihedral_angle_d10.61781398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.368680.2566234X-RAY DIFFRACTION5.63
2.36-2.420.3259330.2451746X-RAY DIFFRACTION17.58
2.42-2.490.3223740.26091473X-RAY DIFFRACTION36.13
2.49-2.570.30681150.29052694X-RAY DIFFRACTION64.35
2.57-2.660.31791810.29873619X-RAY DIFFRACTION87.96
2.66-2.770.30371730.29124072X-RAY DIFFRACTION95.95
2.77-2.90.34441900.27813938X-RAY DIFFRACTION95.69
2.9-3.050.35341720.26133991X-RAY DIFFRACTION95.7
3.05-3.240.2881740.25574034X-RAY DIFFRACTION95.75
3.24-3.490.27591810.22423979X-RAY DIFFRACTION95.41
3.49-3.840.23191660.20363953X-RAY DIFFRACTION94.86
3.84-4.40.2091710.16723903X-RAY DIFFRACTION94.09
4.4-5.540.20521800.15673944X-RAY DIFFRACTION94.33
5.54-46.270.28111730.20453997X-RAY DIFFRACTION96.15
Refinement TLS params.Method: refined / Origin x: 15.4797987083 Å / Origin y: 10.3615407394 Å / Origin z: -4.61865482475 Å
111213212223313233
T0.0598996328948 Å20.00141001579209 Å20.0169971038752 Å2-0.117546359564 Å2-0.0127800818147 Å2--0.14164368825 Å2
L0.0903975283298 °2-0.0138482053781 °20.109827775408 °2-0.0983001224101 °20.0781210643239 °2--0.629316649826 °2
S0.00236247085173 Å °0.0156649677313 Å °0.00915331634558 Å °-0.00535014322117 Å °0.0187128951316 Å °-0.0200868401484 Å °-0.00970557739205 Å °0.0253396647905 Å °3.94762280261E-13 Å °
Refinement TLS groupSelection details: all

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