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- PDB-6pft: rsEGFP2 with a chlorinated chromophore in the non-fluorescent off... -

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Basic information

Entry
Database: PDB / ID: 6pft
TitlersEGFP2 with a chlorinated chromophore in the non-fluorescent off-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Green 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: 1.45 Å
AuthorsChang, J. / Romei, M.G. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins.
Authors: Chang, J. / Romei, M.G. / Boxer, S.G.
History
DepositionJun 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 1, 2020Group: Author supporting evidence / Polymer sequence / Structure summary
Category: chem_comp / entity_poly / pdbx_audit_support
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Oct 11, 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 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

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6632
Polymers28,5671
Non-polymers961
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.014, 62.716, 68.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein /


Mass: 28566.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 309 / 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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 1.76 M ammonium sulfate, 0.1 M HEPES; Cryoprotectant 1 M sucrose, 1.7 M ammonium sulfate, 0.1 M HEPES.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.305053 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305053 Å / Relative weight: 1
ReflectionResolution: 1.45→34.309 Å / Num. obs: 38992 / % possible obs: 98.16 % / Redundancy: 2 % / Biso Wilson estimate: 17.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.008496 / Rrim(I) all: 0.01201 / Net I/σ(I): 21.46
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 2 % / Rmerge(I) obs: 0.08949 / Mean I/σ(I) obs: 5.52 / Num. unique obs: 3674 / CC1/2: 0.982 / Rrim(I) all: 0.1266 / % possible all: 93.61

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.45→34.309 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.1758 2966 4.01 %
Rwork0.1503 --
obs0.1513 38991 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→34.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 5 309 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022063
X-RAY DIFFRACTIONf_angle_d1.6492814
X-RAY DIFFRACTIONf_dihedral_angle_d19.938764
X-RAY DIFFRACTIONf_chiral_restr0.11305
X-RAY DIFFRACTIONf_plane_restr0.012369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47380.24531300.20313185X-RAY DIFFRACTION92
1.4738-1.49920.24831400.19953258X-RAY DIFFRACTION94
1.4992-1.52650.27351380.19093285X-RAY DIFFRACTION96
1.5265-1.55580.2211370.17853337X-RAY DIFFRACTION96
1.5558-1.58760.19831380.1713303X-RAY DIFFRACTION96
1.5876-1.62210.24421390.16813329X-RAY DIFFRACTION97
1.6221-1.65980.18371430.16363382X-RAY DIFFRACTION97
1.6598-1.70130.20651390.16673366X-RAY DIFFRACTION98
1.7013-1.74730.19291400.15913381X-RAY DIFFRACTION99
1.7473-1.79870.19021370.15223405X-RAY DIFFRACTION99
1.7987-1.85680.191440.153452X-RAY DIFFRACTION99
1.8568-1.92320.16941460.1433415X-RAY DIFFRACTION100
1.9232-2.00010.14921430.13493425X-RAY DIFFRACTION100
2.0001-2.09120.18761430.13513451X-RAY DIFFRACTION100
2.0912-2.20140.18621460.13683402X-RAY DIFFRACTION99
2.2014-2.33930.15051430.14193444X-RAY DIFFRACTION100
2.3393-2.51990.17091460.13863463X-RAY DIFFRACTION100
2.5199-2.77330.17621400.14793407X-RAY DIFFRACTION100
2.7733-3.17440.17711470.15493454X-RAY DIFFRACTION100
3.1744-3.99850.13071430.13623423X-RAY DIFFRACTION99
3.9985-34.31910.18641440.16153443X-RAY DIFFRACTION100
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)
14.08732.2303-1.27991.2166-0.70510.4133-0.2310.59920.4375-0.0793-0.1346-0.0922-0.47110.34640.02260.37570.0169-0.0610.31130.12290.4737-23.772723.4126-10.4486
21.07391.25820.14118.91870.67310.81710.02210.0118-0.0073-0.17-0.14740.46040.1426-0.09590.11780.17350.00280.00590.1724-0.00440.1536-35.96931.1260.1625
31.70460.29090.02142.2993-0.01151.4426-0.0418-0.0174-0.02730.10380.03-0.01450.0682-0.04450.02980.12280.01360.00160.13490.00030.1201-29.23363.36123.9941
44.25741.3857-1.25931.9061-0.2281.76670.04430.2720.0539-0.0689-0.0289-0.213-0.17020.1015-0.04380.14370.00380.0020.20140.03040.1898-16.764215.4663-9.7675
50.8498-0.0543-0.06162.8405-0.72980.89070.07150.1607-0.0321-0.1321-0.1199-0.0580.07830.0040.04430.16370.02520.00350.1845-0.01150.1369-27.05132.1429-9.9863
61.1004-0.85420.01568.21010.02051.11820.0520.1133-0.0215-0.0096-0.09950.39140.0574-0.12610.06590.10660.0080.00480.1769-0.0090.1433-34.58073.749-5.6984
71.2950.0438-0.03331.9059-0.00551.2988-0.1576-0.0751-0.26460.14750.045-0.11240.35440.10940.10590.29760.03090.02670.18420.00510.1979-24.2002-11.66024.9789
81.8556-0.7468-0.30113.8124-1.84264.41380.17810.27860.0287-0.2835-0.1117-0.1290.07280.0901-0.09450.19810.0230.01570.1963-0.01540.191-18.7599-0.1387-11.8067
91.4015-0.39560.10712.4563-0.7321.31030.06380.2033-0.0312-0.2225-0.0598-0.00020.17040.08240.03390.13410.01790.02580.1588-0.02150.1322-23.41490.8776-11.1421
101.49770.11010.18111.3477-0.66832.9108-0.111-0.262-0.03350.246-0.0162-0.09760.07270.2570.11070.18420.0383-0.00650.102-0.02440.1388-22.18993.99796.5838
111.2226-0.0328-0.94211.0678-0.4582.631-0.0534-0.02230.07260.06970.0198-0.1735-0.07420.18890.05650.13420.0172-0.01140.1641-0.00590.1504-20.39137.16413.1496
122.8558-4.171-1.56266.44450.6849.4550.0004-0.0646-0.5124-0.4292-0.31540.24820.1842-0.2010.20320.3596-0.00030.01350.3451-0.02820.361-1.281416.6603-15.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 129 )
7X-RAY DIFFRACTION7chain 'A' and (resid 130 through 148 )
8X-RAY DIFFRACTION8chain 'A' and (resid 149 through 171 )
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 199 )
10X-RAY DIFFRACTION10chain 'A' and (resid 200 through 217 )
11X-RAY DIFFRACTION11chain 'A' and (resid 218 through 228 )
12X-RAY DIFFRACTION12chain 'A' and (resid 229 through 239 )

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