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- PDB-6og9: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3... -

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Basic information

Entry
Database: PDB / ID: 6og9
TitleCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)
ComponentsCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)
KeywordsFLUORESCENT PROTEIN / GFP
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsLin, C.-Y. / Deng, A. / 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
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)56,1932
Polymers56,1932
Non-polymers00
Water12,556697
1
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)28,0961
Polymers28,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(3,5-F2Y), H148D; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)28,0961
Polymers28,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.123, 70.131, 61.100
Angle α, β, γ (deg.)90.00, 96.31, 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(3,5-F2Y), H148D; circular permutant (50-51)


Mass: 28096.254 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 35.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM sodium acetate, pH 5.0, 100 mM NaCl, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.798→36.594 Å / Num. obs: 38844 / % possible obs: 98.78 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1052 / Rpim(I) all: 0.06394 / Rrim(I) all: 0.1234 / Net I/σ(I): 12.58
Reflection shellResolution: 1.798→1.863 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.7413 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 3808 / CC1/2: 0.644 / Rpim(I) all: 0.4528 / Rrim(I) all: 0.8709 / % possible all: 97.64

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zf3

4zf3


Resolution: 1.798→36.594 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4
RfactorNum. reflection% reflection
Rfree0.1998 1935 5 %
Rwork0.1682 --
obs0.1698 38680 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→36.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 697 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033900
X-RAY DIFFRACTIONf_angle_d0.6695340
X-RAY DIFFRACTIONf_dihedral_angle_d5.1813161
X-RAY DIFFRACTIONf_chiral_restr0.05597
X-RAY DIFFRACTIONf_plane_restr0.003701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7982-1.84320.26321330.22642534X-RAY DIFFRACTION97
1.8432-1.89310.26061390.2262636X-RAY DIFFRACTION100
1.8931-1.94880.30881300.28222471X-RAY DIFFRACTION94
1.9488-2.01160.23021410.18622687X-RAY DIFFRACTION100
2.0116-2.08350.20931380.19042615X-RAY DIFFRACTION100
2.0835-2.1670.21651400.17342643X-RAY DIFFRACTION100
2.167-2.26560.25911350.19072555X-RAY DIFFRACTION95
2.2656-2.3850.19841380.1682620X-RAY DIFFRACTION100
2.385-2.53440.211400.17562658X-RAY DIFFRACTION100
2.5344-2.730.20051390.17382639X-RAY DIFFRACTION100
2.73-3.00460.20251410.16482674X-RAY DIFFRACTION100
3.0046-3.43910.15351400.1432663X-RAY DIFFRACTION100
3.4391-4.33180.16941390.13292645X-RAY DIFFRACTION99
4.3318-36.60160.1621420.13952705X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.3154 Å / Origin y: -0.4268 Å / Origin z: 76.4031 Å
111213212223313233
T0.1046 Å2-0.0062 Å20.0093 Å2-0.0856 Å2-0.0121 Å2--0.1051 Å2
L0.248 °2-0.0479 °20.0736 °2-0.3089 °2-0.2593 °2--0.8531 °2
S-0.0093 Å °0.0073 Å °-0.0088 Å °-0.0009 Å °-0.0045 Å °-0.0038 Å °0.026 Å °-0.0233 Å °0.017 Å °
Refinement TLS groupSelection details: all

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