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- PDB-6un4: Crystal structure of rsEGFP2, Y67(3-ClY), Y107(3-ClY) -

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Basic information

Entry
Database: PDB / ID: 6un4
TitleCrystal structure of rsEGFP2, Y67(3-ClY), Y107(3-ClY)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / photoswitchable fluorescent 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsLin, C.-Y. / Romei, M.G. / Boxer, S.G. / Chang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J Photochem Photobiol A Chem / Year: 2020
Title: Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms.
Authors: Romei, M.G. / Lin, C.Y. / Boxer, S.G.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / Item: _citation.page_first
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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_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.id / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_mod_residue.label_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6972
Polymers28,6011
Non-polymers961
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.341, 61.848, 69.057
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: 28601.094 Da / Num. of mol.: 1 / Mutation: F64L,Q69L,V163S,A206K,H231L
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 80 mM HEPES, pH 8.1, 1.84 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.119499 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.119499 Å / Relative weight: 1
ReflectionResolution: 1.499→34.529 Å / Num. obs: 35265 / % possible obs: 98.1 % / Redundancy: 13.247 % / Biso Wilson estimate: 22.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.055 / Χ2: 1.027 / Net I/σ(I): 24.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.5413.1191.8741.3232929263125100.6751.94995.4
1.54-1.5813.3461.41.8932965253224700.7931.45497.6
1.58-1.6313.3371.1032.4432583250424430.8681.14797.6
1.63-1.6813.1920.833.2731265241423700.9230.86398.2
1.68-1.7312.9360.6014.4829352232122690.9550.62597.8
1.73-1.7912.5460.4745.427664228722050.9650.49496.4
1.79-1.8613.8810.3597.6230080219121670.9840.37398.9
1.86-1.9413.7680.24810.7828637209720800.9920.25799.2
1.94-2.0213.6910.17314.8627738203620260.9960.17999.5
2.02-2.1213.5110.13618.4426063194019290.9970.14299.4
2.12-2.2313.2420.10223.6724352186418390.9980.10698.7
2.23-2.3712.5680.08527.4721492175417100.9980.08997.5
2.37-2.5313.2520.06834.9321428165116170.9990.07197.9
2.53-2.7414.0650.05543.9921688155115420.9990.05799.4
2.74-313.8170.04654.1719800144414330.9990.04799.2
3-3.3513.010.03273.21168221298129310.03499.6
3.35-3.8712.4780.02585.56145491166116610.026100
3.87-4.7411.9760.0296.651125799394010.02194.7
4.74-6.713.5970.02102.51070178878710.0299.9
6.7-34.52912.3480.017106.23568046746010.01798.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13rc2_2986refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFR

6pfr


Resolution: 1.499→34.529 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.1975 1763 5 %
Rwork0.1782 --
obs0.1792 35265 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.04 Å2 / Biso mean: 33.1989 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 1.499→34.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 21 239 2224
Biso mean--44.47 39.5 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4991-1.53970.3821280.3386243994
1.5397-1.5850.30321330.2912251397
1.585-1.63610.30751330.2628253198
1.6361-1.69460.31121340.2397255298
1.6946-1.76250.26931330.2249251597
1.7625-1.84270.23031350.206255398
1.8427-1.93980.22521350.186258399
1.9398-2.06130.19061380.1809261899
2.0613-2.22050.20991350.1735258399
2.2205-2.44390.18791350.1753256497
2.4439-2.79740.21171390.1788262899
2.7974-3.52380.17451400.16522674100
3.5238-34.5290.16721450.1558274998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3325-0.8439-2.4081.41381.25612.6160.2017-0.05530.47610.1201-0.0481-0.1888-0.42030.4877-0.13620.3226-0.0571-0.03640.27210.02610.4198-22.671624.4384-9.8996
20.87970.0643-0.25011.6484-0.24871.6251-0.05230.009-0.06330.036-0.00070.10410.1114-0.02250.05020.17280.00130.00060.2125-0.02280.2594-28.15623.5122-2.4063
30.3599-0.19280.22680.92390.79941.35750.04030.0797-0.1918-0.1801-0.25030.88230.0126-0.27320.18290.2068-0.0096-0.00240.2732-0.04160.3499-35.9826.4785-5.8029
43.04350.32640.16433.7926-0.02854.9764-0.0763-0.1513-0.82670.37010.0543-0.06440.7312-0.20720.02280.32810.04270.0870.20990.0060.3799-25.2888-11.85654.789
51.44960.4559-1.3652.6948-1.3816.8625-0.0540.2425-0.0684-0.3811-0.1054-0.19480.51160.28940.05970.26870.02840.03240.2547-0.05690.2498-20.0151-0.5455-12.7565
62.1756-0.90470.534.8145-2.63663.2745-0.03810.0414-0.2087-0.03140.05880.12380.16010.0522-0.01830.21310.00130.01810.2278-0.07220.2473-22.6992-0.7549-9.6915
72.35630.9421-1.72991.3141-1.21844.8782-0.0095-0.2827-0.01810.1654-0.0592-0.08340.02050.33340.14290.18970.0223-0.00120.2087-0.00440.2369-22.5564.92096.392
82.55392.0940.52962.5711.060.69290.23840.1159-0.231-0.5786-0.0953-0.06960.48780.41350.00630.51150.019-0.03690.6454-0.03390.6513-1.152915.8637-14.7858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 12 )A-7 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 108 )A13 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 128 )A109 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 148 )A129 - 148
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 171 )A149 - 171
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 199 )A172 - 199
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 228 )A200 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 239 )A229 - 239

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