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- PDB-6oga: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3... -

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Basic information

Entry
Database: PDB / ID: 6oga
TitleCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
ComponentsCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
KeywordsFLUORESCENT PROTEIN / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / ACETATE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLin, C.-Y. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.
Authors: Lin, C.Y. / Boxer, S.G.
History
DepositionApr 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7328
Polymers56,2782
Non-polymers4536
Water6,233346
1
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4745
Polymers28,1391
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2573
Polymers28,1391
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 68.600, 61.450
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3-Br1Y), H148D; circular permutant (50-51)


Mass: 28139.170 Da / Num. of mol.: 2
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM sodium acetate, pH 5.0, 100 mM NaCl, 7-8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→34.3 Å / Num. obs: 54833 / % possible obs: 98.33 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07353 / Rpim(I) all: 0.03313 / Rrim(I) all: 0.08091 / Net I/σ(I): 13.38
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 5471 / CC1/2: 0.592 / Rpim(I) all: 0.4877 / Rrim(I) all: 1.199 / % possible all: 98.75

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zf3

4zf3


Resolution: 1.6→34.3 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.1862 2742 5 %
Rwork0.1612 --
obs0.1625 54826 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 30 346 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073856
X-RAY DIFFRACTIONf_angle_d0.8665231
X-RAY DIFFRACTIONf_dihedral_angle_d13.822270
X-RAY DIFFRACTIONf_chiral_restr0.06581
X-RAY DIFFRACTIONf_plane_restr0.005687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.62750.31781370.28132602X-RAY DIFFRACTION99
1.6275-1.65710.34061360.27012596X-RAY DIFFRACTION99
1.6571-1.6890.27371360.24842581X-RAY DIFFRACTION99
1.689-1.72350.28531380.23822609X-RAY DIFFRACTION98
1.7235-1.76090.25691370.23052604X-RAY DIFFRACTION98
1.7609-1.80190.26511340.22142553X-RAY DIFFRACTION97
1.8019-1.8470.26661350.21192555X-RAY DIFFRACTION97
1.847-1.89690.21651370.20032606X-RAY DIFFRACTION99
1.8969-1.95270.21971380.17232619X-RAY DIFFRACTION99
1.9527-2.01570.17891370.1532614X-RAY DIFFRACTION99
2.0157-2.08780.18341360.15162590X-RAY DIFFRACTION98
2.0878-2.17130.19211350.14852563X-RAY DIFFRACTION97
2.1713-2.27010.18441370.15252591X-RAY DIFFRACTION98
2.2701-2.38980.16821380.1562619X-RAY DIFFRACTION99
2.3898-2.53950.18621380.15482636X-RAY DIFFRACTION100
2.5395-2.73550.17051380.15582604X-RAY DIFFRACTION98
2.7355-3.01060.17931360.15542589X-RAY DIFFRACTION98
3.0106-3.44590.16011400.14072669X-RAY DIFFRACTION99
3.4459-4.34010.14661370.13532600X-RAY DIFFRACTION98
4.3401-34.30790.17821420.15582684X-RAY DIFFRACTION99
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)
11.25570.0258-0.07011.2122-0.00180.6752-0.03340.03240.0331-0.00130.0104-0.04530.03260.02170.02550.21530.01010.00230.161-0.00480.16296.263410.55940.7922
21.72640.0003-0.43711.3655-0.51492.0774-0.1064-0.2565-0.07140.02640.0323-0.08710.09040.22770.04890.18260.01290.00940.1980.00270.141612.813621.654528.5516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:242 )A1 - 242
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:243 )B2 - 243

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