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- PDB-6ogc: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2... -

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Basic information

Entry
Database: PDB / ID: 6ogc
TitleCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-F2Y), H148D; circular permutant (50-51)
ComponentsCrystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-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: 1.178 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
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-F2Y), H148D; circular permutant (50-51)
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-F2Y), H148D; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)56,1932
Polymers56,1932
Non-polymers00
Water11,800655
1
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(2,3-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(2,3-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)52.275, 68.866, 60.968
Angle α, β, γ (deg.)90.00, 100.34, 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(2,3-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.: 655 / 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: 1.92 Å3/Da / Density % sol: 35.98 %
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: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.178→36.5 Å / Num. obs: 134742 / % possible obs: 95 % / Redundancy: 13.1 % / Biso Wilson estimate: 9.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04828 / Rpim(I) all: 0.01365 / Rrim(I) all: 0.05023 / Net I/σ(I): 29.19
Reflection shellResolution: 1.178→1.221 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.5514 / Mean I/σ(I) obs: 3.65 / Num. unique obs: 11199 / CC1/2: 0.905 / Rpim(I) all: 0.1726 / Rrim(I) all: 0.5796 / % possible all: 80.44

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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: 1.178→36.5 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.48
RfactorNum. reflection% reflection
Rfree0.1609 6639 4.99 %
Rwork0.1434 --
obs0.1443 132929 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.178→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 0 655 4291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144133
X-RAY DIFFRACTIONf_angle_d1.3975654
X-RAY DIFFRACTIONf_dihedral_angle_d19.2261511
X-RAY DIFFRACTIONf_chiral_restr0.114619
X-RAY DIFFRACTIONf_plane_restr0.01759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1784-1.19180.1981360.18072567X-RAY DIFFRACTION58
1.1918-1.20580.17232060.14963938X-RAY DIFFRACTION89
1.2058-1.22050.22492180.17114134X-RAY DIFFRACTION93
1.2205-1.2360.22180.18024151X-RAY DIFFRACTION94
1.236-1.25220.16252260.1434287X-RAY DIFFRACTION97
1.2522-1.26940.2922060.25923785X-RAY DIFFRACTION86
1.2694-1.28750.17562260.13414309X-RAY DIFFRACTION98
1.2875-1.30670.19652180.15694167X-RAY DIFFRACTION94
1.3067-1.32710.16332250.12614276X-RAY DIFFRACTION97
1.3271-1.34890.16362270.13064309X-RAY DIFFRACTION97
1.3489-1.37220.22382110.1854104X-RAY DIFFRACTION92
1.3722-1.39710.1732220.14274238X-RAY DIFFRACTION97
1.3971-1.4240.15582310.1184371X-RAY DIFFRACTION99
1.424-1.45310.17472250.15764305X-RAY DIFFRACTION96
1.4531-1.48470.19052240.14834248X-RAY DIFFRACTION96
1.4847-1.51920.17262280.12864314X-RAY DIFFRACTION98
1.5192-1.55720.17012180.12574130X-RAY DIFFRACTION94
1.5572-1.59930.13642260.11084288X-RAY DIFFRACTION97
1.5993-1.64630.1562330.11564412X-RAY DIFFRACTION99
1.6463-1.69950.14052310.12214406X-RAY DIFFRACTION99
1.6995-1.76020.17912290.13424349X-RAY DIFFRACTION99
1.7602-1.83070.14362310.1334394X-RAY DIFFRACTION99
1.8307-1.9140.17552280.14134315X-RAY DIFFRACTION97
1.914-2.01490.1542210.13764197X-RAY DIFFRACTION95
2.0149-2.14110.14992140.14174318X-RAY DIFFRACTION97
2.1411-2.30640.14792310.14124349X-RAY DIFFRACTION98
2.3064-2.53850.15262330.15114439X-RAY DIFFRACTION99
2.5385-2.90570.16282280.1584306X-RAY DIFFRACTION96
2.9057-3.66030.14212320.14784418X-RAY DIFFRACTION99
3.6603-36.51750.15392370.13944466X-RAY DIFFRACTION98

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