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- PDB-4jfg: Crystal structure of sfGFP-66-HqAla -

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Basic information

Entry
Database: PDB / ID: 4jfg
TitleCrystal structure of sfGFP-66-HqAla
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / 11-stranded beta-barrel
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
: / quinolin-8-ol / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsWang, J. / Liu, X. / Li, J. / Zhang, W. / Hu, M. / Zhou, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Significant expansion of the fluorescent protein chromophore through the genetic incorporation of a metal-chelating unnatural amino acid.
Authors: Liu, X. / Li, J. / Hu, C. / Zhou, Q. / Zhang, W. / Hu, M. / Zhou, J. / Wang, J.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein
F: Green fluorescent protein
G: Green fluorescent protein
H: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,72247
Polymers221,4418
Non-polymers5,28139
Water2,342130
1
A: Green fluorescent protein
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,98014
Polymers55,3602
Non-polymers1,61912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Green fluorescent protein
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58111
Polymers55,3602
Non-polymers1,2219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Green fluorescent protein
G: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58111
Polymers55,3602
Non-polymers1,2219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Green fluorescent protein
H: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58111
Polymers55,3602
Non-polymers1,2219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.174, 148.901, 161.350
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: 27680.113 Da / Num. of mol.: 8
Mutation: S30R, Y39N, Q80R, F99S, N105T, Y145F, M153T, V163A, I171V, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical
ChemComp-HQY / quinolin-8-ol / 8-hydroxyquinoline


Mass: 145.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H7NO
#3: Chemical...
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Cs
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15-20% polyethylene glycol (PEG) 3350, 0.13-0.18M CsCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIHAKU Satun944HG / Detector: CCD / Date: Feb 3, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 36392 / % possible obs: 84.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3→3.11 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 3.001→21.841 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.312 1751 5.09 %
Rwork0.2588 --
obs0.2615 34374 79.73 %
all-36392 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3798 Å20 Å20 Å2
2--5.2437 Å2-0 Å2
3---4.3425 Å2
Refinement stepCycle: LAST / Resolution: 3.001→21.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13992 0 119 130 14241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414461
X-RAY DIFFRACTIONf_angle_d0.98319483
X-RAY DIFFRACTIONf_dihedral_angle_d14.8565213
X-RAY DIFFRACTIONf_chiral_restr0.0572117
X-RAY DIFFRACTIONf_plane_restr0.0032543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0013-3.08220.42241630.33063019X-RAY DIFFRACTION98
3.0822-3.17270.35641890.28273058X-RAY DIFFRACTION99
3.1727-3.27470.34811510.28323133X-RAY DIFFRACTION100
3.2747-3.39140.32881510.24923130X-RAY DIFFRACTION100
3.3914-3.52660.31691670.26743065X-RAY DIFFRACTION98
3.5266-3.68640.5102590.41621299X-RAY DIFFRACTION50
3.8797-4.12130.35091080.28971970X-RAY DIFFRACTION66
4.1213-4.4370.29461930.20263104X-RAY DIFFRACTION99
4.437-4.87910.2165620.20051217X-RAY DIFFRACTION39
4.8791-5.57480.22431610.20353170X-RAY DIFFRACTION100
5.5748-6.98530.29851570.26753194X-RAY DIFFRACTION99
6.9853-21.84120.31531900.28983264X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -21.4139 Å / Origin y: -49.993 Å / Origin z: -57.6708 Å
111213212223313233
T0.0082 Å2-0.0211 Å20.034 Å2-0.0458 Å2-0.0043 Å2--0.0355 Å2
L-0.0163 °20.0532 °20.02 °2-0.0953 °20.0491 °2--0.0695 °2
S-0.029 Å °0.002 Å °0.0057 Å °-0.0343 Å °0.0003 Å °-0.0349 Å °-0.0213 Å °-0.0472 Å °-0.0413 Å °
Refinement TLS groupSelection details: ALL

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