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- PDB-6pfr: rsEGFP2 with a chlorinated chromophore in the fluorescent on-state -

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Basic information

Entry
Database: PDB / ID: 6pfr
TitlersEGFP2 with a chlorinated chromophore in the fluorescent on-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: 1.51 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 2.0Oct 23, 2019Group: Data collection / Polymer sequence / Structure summary
Category: chem_comp / entity_poly
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
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 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 2.3Nov 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


Theoretical massNumber of molelcules
Total (without water)28,5671
Polymers28,5671
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.699, 62.489, 67.591
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.88 Å3/Da / Density % sol: 34.44 %
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.
Temp details: Room temp

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.51→39.371 Å / Num. obs: 32194 / % possible obs: 93.52 % / Redundancy: 2 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01152 / Rrim(I) all: 0.0163 / Net I/σ(I): 19.5
Reflection shellResolution: 1.51→1.564 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3537 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 3364 / CC1/2: 0.854 / Rrim(I) all: 0.5002 / % possible all: 99.61

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Processing

Software
NameVersionClassification
PHENIX1.13rc2_2986refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTX

5dtx


Resolution: 1.51→39.371 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35
RfactorNum. reflection% reflection
Rfree0.2115 1610 5 %
Rwork0.1877 --
obs0.1889 32177 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.51→39.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 0 216 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071987
X-RAY DIFFRACTIONf_angle_d0.7812697
X-RAY DIFFRACTIONf_dihedral_angle_d15.0491182
X-RAY DIFFRACTIONf_chiral_restr0.058291
X-RAY DIFFRACTIONf_plane_restr0.006349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5098-1.55420.37931380.34052656X-RAY DIFFRACTION100
1.5542-1.60440.29041280.28522506X-RAY DIFFRACTION99
1.6044-1.66170.2789940.27161725X-RAY DIFFRACTION77
1.6617-1.72820.35781210.25092177X-RAY DIFFRACTION80
1.7282-1.80690.27391130.22932297X-RAY DIFFRACTION85
1.8069-1.90210.24081440.21152677X-RAY DIFFRACTION100
1.9021-2.02130.23571340.19262723X-RAY DIFFRACTION100
2.0213-2.17740.22361510.18122692X-RAY DIFFRACTION100
2.1774-2.39650.22781420.1782717X-RAY DIFFRACTION100
2.3965-2.74320.18411460.18152719X-RAY DIFFRACTION99
2.7432-3.45580.19791480.17862773X-RAY DIFFRACTION100
3.4558-39.38420.18061510.16722905X-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)
13.3453.2532-2.85024.807-4.43544.1771-0.24790.76340.33730.01560.0142-0.096-0.56840.62020.38540.4263-0.02780.00340.40860.08720.7085-24.345222.8905-10.4071
24.21252.543-0.12732.2693-0.21891.24080.04420.03360.02780.1718-0.09510.22350.0518-0.19230.08270.1940.0160.00430.2192-0.00320.2444-34.44522.532.2397
31.3949-0.30220.05640.9844-0.20471.60170.01380.11370.05120.0026-0.0644-0.1366-0.00050.01110.05750.15880.0211-0.00770.17920.00310.2647-25.0625.18-3.8719
41.24651.60070.06896.9389-0.5921.6746-0.01430.12510.0199-0.03550.03070.52420.1202-0.1778-0.05230.12330.0176-0.00220.1929-0.00450.2085-34.44943.5337-5.7886
53.2881-1.23280.12910.6361-0.46574.3186-0.2684-0.2071-0.54870.01060.1214-0.17760.42890.12240.02440.29360.04650.0230.19490.02960.3381-23.6644-11.1685.0894
62.9111-0.9171-0.99995.9915-2.8566.5750.25020.32070.1543-0.4756-0.2454-0.33240.08690.2086-0.02690.24150.05460.04050.2283-0.00340.2988-18.6056-0.0109-11.9131
72.5222-1.94290.83214.0215-2.60713.08990.03980.27150.1208-0.0176-0.1801-0.30250.05430.06960.0570.21340.0136-0.00720.2105-0.02250.2672-22.92140.6353-11.2088
82.93421.0085-2.33271.1186-1.82367.8552-0.0535-0.33230.05940.3319-0.0687-0.2032-0.24370.30730.0120.26050.0623-0.03460.1208-0.05080.3097-22.22764.07296.6487
93.59121.1805-3.25181.8035-1.24814.9005-0.11580.07450.0852-0.36040.0009-0.27530.00510.4037-0.07350.26860.0127-0.00940.31990.0160.3995-10.736211.7188-5.8494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 148 )
6X-RAY DIFFRACTION6chain 'A' and (resid 149 through 171 )
7X-RAY DIFFRACTION7chain 'A' and (resid 172 through 199 )
8X-RAY DIFFRACTION8chain 'A' and (resid 200 through 217 )
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 239 )

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