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- PDB-7dmx: Photocleavable Fluorescent Protein in green form -

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Basic information

Entry
Database: PDB / ID: 7dmx
TitlePhotocleavable Fluorescent Protein in green form
ComponentsPhoCl green
KeywordsFLUORESCENT PROTEIN / PhoCl / Green form / Photocleavable
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWen, Y. / Lemieux, M.J.
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 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 23, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhoCl green
B: PhoCl green
C: PhoCl green
D: PhoCl green


Theoretical massNumber of molelcules
Total (without water)110,0214
Polymers110,0214
Non-polymers00
Water7,548419
1
A: PhoCl green


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PhoCl green


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PhoCl green


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PhoCl green


Theoretical massNumber of molelcules
Total (without water)27,5051
Polymers27,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.360, 112.760, 144.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 12 or (resid 13...
21(chain B and (resid 3 through 12 or (resid 13...
31(chain C and (resid 3 through 23 or resid 25...
41(chain D and (resid 3 through 12 or (resid 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPROPRO(chain A and (resid 3 through 12 or (resid 13...AA3 - 122 - 11
12GLUGLUGLUGLU(chain A and (resid 3 through 12 or (resid 13...AA1312
13ILEILEPROPRO(chain A and (resid 3 through 12 or (resid 13...AA3 - 2422 - 239
14ILEILEPROPRO(chain A and (resid 3 through 12 or (resid 13...AA3 - 2422 - 239
15ILEILEPROPRO(chain A and (resid 3 through 12 or (resid 13...AA3 - 2422 - 239
16ILEILEPROPRO(chain A and (resid 3 through 12 or (resid 13...AA3 - 2422 - 239
21ILEILEPROPRO(chain B and (resid 3 through 12 or (resid 13...BB3 - 122 - 11
22GLUGLUGLUGLU(chain B and (resid 3 through 12 or (resid 13...BB1312
23VALVALPROPRO(chain B and (resid 3 through 12 or (resid 13...BB2 - 2421 - 239
24VALVALPROPRO(chain B and (resid 3 through 12 or (resid 13...BB2 - 2421 - 239
25VALVALPROPRO(chain B and (resid 3 through 12 or (resid 13...BB2 - 2421 - 239
26VALVALPROPRO(chain B and (resid 3 through 12 or (resid 13...BB2 - 2421 - 239
31ILEILETYRTYR(chain C and (resid 3 through 23 or resid 25...CC3 - 232 - 22
32ASPASPASNASN(chain C and (resid 3 through 23 or resid 25...CC25 - 4424 - 43
33LYSLYSLYSLYS(chain C and (resid 3 through 23 or resid 25...CC4544
34ILEILEPROPRO(chain C and (resid 3 through 23 or resid 25...CC3 - 2422 - 239
35ILEILEPROPRO(chain C and (resid 3 through 23 or resid 25...CC3 - 2422 - 239
36ILEILEPROPRO(chain C and (resid 3 through 23 or resid 25...CC3 - 2422 - 239
37ILEILEPROPRO(chain C and (resid 3 through 23 or resid 25...CC3 - 2422 - 239
38ILEILEPROPRO(chain C and (resid 3 through 23 or resid 25...CC3 - 2422 - 239
41ILEILEPROPRO(chain D and (resid 3 through 12 or (resid 13...DD3 - 122 - 11
42GLUGLUGLUGLU(chain D and (resid 3 through 12 or (resid 13...DD1312
43ILEILEARGARG(chain D and (resid 3 through 12 or (resid 13...DD3 - 2432 - 240

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Components

#1: Protein
PhoCl green


Mass: 27505.221 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
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: PSI 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: 2.1→44.39 Å / Num. obs: 57043 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 9.73
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.709 / Num. unique obs: 9153 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQK

2hqk


Resolution: 2.1→44.39 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2000 4.66 %
Rwork0.2054 40918 -
obs0.2075 42918 73.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.43 Å2 / Biso mean: 33.01 Å2 / Biso min: 10.22 Å2
Refinement stepCycle: final / Resolution: 2.1→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6775 0 0 419 7194
Biso mean---33.67 -
Num. residues----845
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2356X-RAY DIFFRACTION7.333TORSIONAL
12B2356X-RAY DIFFRACTION7.333TORSIONAL
13C2356X-RAY DIFFRACTION7.333TORSIONAL
14D2356X-RAY DIFFRACTION7.333TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.5086110.26782132245
2.16-2.210.3531280.224558261015
2.21-2.280.347510.23991040109127
2.28-2.350.3502860.24921779186545
2.35-2.440.31361410.25282877301874
2.44-2.530.29531800.25613676385693
2.54-2.650.26771880.2423862405098
2.65-2.790.27981890.24843847403698
2.79-2.960.28671890.25213878406798
2.96-3.190.28791850.23093783396896
3.19-3.510.26541860.20363820400696
3.52-4.020.23531890.17813853404296
4.02-5.070.18311870.14793828401595
5.07-44.390.19731900.18183880407092

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