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- PDB-6og8: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D... -

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Entry
Database: PDB / ID: 6og8
TitleCrystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally incorporated 3-F1Y; circular permutant (50-51)
ComponentsCrystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally incorporated 3-F1Y; 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 / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 1, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, H148D with globally incorporated 3-F1Y; circular permutant (50-51)
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally incorporated 3-F1Y; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)56,4442
Polymers56,4442
Non-polymers00
Water13,097727
1
B: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally incorporated 3-F1Y; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)28,2221
Polymers28,2221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D with globally incorporated 3-F1Y; circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)28,2221
Polymers28,2221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.073, 70.072, 61.072
Angle α, β, γ (deg.)90.00, 95.93, 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, H148D with globally incorporated 3-F1Y; circular permutant (50-51)


Mass: 28222.182 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.: 727 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.85 %
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: 1.599→27.283 Å / Num. obs: 54415 / % possible obs: 97.18 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06816 / Rpim(I) all: 0.04259 / Rrim(I) all: 0.08065 / Net I/σ(I): 14.17
Reflection shellResolution: 1.599→1.656 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6034 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4373 / CC1/2: 0.543 / Rpim(I) all: 0.5059 / Rrim(I) all: 0.7933 / % possible all: 78.6

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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: 1.599→27.283 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1904 2721 5 %
Rwork0.1589 --
obs0.1604 54410 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→27.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 727 4348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084135
X-RAY DIFFRACTIONf_angle_d1.0465695
X-RAY DIFFRACTIONf_dihedral_angle_d5.983208
X-RAY DIFFRACTIONf_chiral_restr0.069629
X-RAY DIFFRACTIONf_plane_restr0.005738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5988-1.62790.32611070.28622033X-RAY DIFFRACTION73
1.6279-1.65920.30751240.25482359X-RAY DIFFRACTION85
1.6592-1.69310.27551350.22392567X-RAY DIFFRACTION92
1.6931-1.72990.23541450.21072741X-RAY DIFFRACTION98
1.7299-1.77010.21981450.18262763X-RAY DIFFRACTION100
1.7701-1.81440.22261460.17692769X-RAY DIFFRACTION100
1.8144-1.86340.20361480.17222813X-RAY DIFFRACTION100
1.8634-1.91820.20421470.17842794X-RAY DIFFRACTION100
1.9182-1.98010.22381470.17772786X-RAY DIFFRACTION100
1.9801-2.05090.19941460.15582787X-RAY DIFFRACTION100
2.0509-2.13290.19411470.15092784X-RAY DIFFRACTION100
2.1329-2.230.17711470.14992784X-RAY DIFFRACTION100
2.23-2.34750.20261460.15222792X-RAY DIFFRACTION100
2.3475-2.49450.17311480.15482803X-RAY DIFFRACTION100
2.4945-2.68690.19761470.16172797X-RAY DIFFRACTION100
2.6869-2.9570.1791490.162823X-RAY DIFFRACTION100
2.957-3.38420.1651470.14262807X-RAY DIFFRACTION100
3.3842-4.26110.16081490.12892815X-RAY DIFFRACTION100
4.2611-27.28680.15111510.13532872X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.6698 Å / Origin y: -21.0603 Å / Origin z: -14.6435 Å
111213212223313233
T0.0742 Å2-0.0027 Å20.0194 Å2-0.0595 Å2-0.0104 Å2--0.0864 Å2
L0.1845 °2-0.0348 °20.1332 °2-0.2968 °2-0.2279 °2--0.7023 °2
S-0.0209 Å °-0.0095 Å °-0.0028 Å °0.0042 Å °0.0036 Å °0.0015 Å °0.0231 Å °-0.024 Å °0.0179 Å °
Refinement TLS groupSelection details: all

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