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- PDB-5yr2: Structure of cpGFP66BPA -

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Basic information

Entry
Database: PDB / ID: 5yr2
TitleStructure of cpGFP66BPA
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Bioluminescence Protein Chromophore Linkage
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: 1.799 Å
AuthorsWang, L. / Kang, F. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Education (China)2017YFA0503704 China
CitationJournal: To Be Published
Title: Structure of cpGFP66BPA
Authors: Wang, L. / Kang, F.
History
DepositionNov 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,9072
Polymers55,9072
Non-polymers00
Water7,512417
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,9531
Polymers27,9531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,9531
Polymers27,9531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.640, 63.709, 69.159
Angle α, β, γ (deg.)90.00, 101.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein


Mass: 27953.359 Da / Num. of mol.: 2 / Mutation: Y163(BPA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Plasmid: PET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A059PIQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP residue TYR 66 has been mutated to unnatural amino acid named 4-Benzoyl-L-phenylalanine. 3 ...UNP residue TYR 66 has been mutated to unnatural amino acid named 4-Benzoyl-L-phenylalanine. 3 residues THR, 4-Benzoyl-L-phenylalanine, GLY constitute the chromophore BF9 163.

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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: 2.09 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350 25%, 0.2M MgCl2,0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 39464 / % possible obs: 98.5 % / Redundancy: 5.6 % / CC1/2: 0.996 / Net I/σ(I): 21.17
Reflection shellResolution: 1.799→1.86 Å / Redundancy: 5.6 % / Num. unique obs: 3883 / CC1/2: 0.912 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GFL

1gfl


Resolution: 1.799→39.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1935 4.91 %RANDOM
Rwork0.168 ---
obs0.1703 39441 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→39.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 0 417 4063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063924
X-RAY DIFFRACTIONf_angle_d1.1485349
X-RAY DIFFRACTIONf_dihedral_angle_d15.1252385
X-RAY DIFFRACTIONf_chiral_restr0.066595
X-RAY DIFFRACTIONf_plane_restr0.006699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7988-1.84380.28481320.23942477X-RAY DIFFRACTION92
1.8438-1.89360.2931520.20292644X-RAY DIFFRACTION98
1.8936-1.94930.25331450.18292657X-RAY DIFFRACTION98
1.9493-2.01230.23861150.1742674X-RAY DIFFRACTION98
2.0123-2.08420.23341290.17672695X-RAY DIFFRACTION98
2.0842-2.16760.22571500.17122656X-RAY DIFFRACTION98
2.1676-2.26630.23261450.17892677X-RAY DIFFRACTION98
2.2663-2.38570.23141310.17672700X-RAY DIFFRACTION99
2.3857-2.53520.23921400.17912696X-RAY DIFFRACTION99
2.5352-2.73090.21891280.17952674X-RAY DIFFRACTION99
2.7309-3.00560.25471420.18782729X-RAY DIFFRACTION99
3.0056-3.44030.19951560.15752701X-RAY DIFFRACTION99
3.4403-4.33350.18481430.14482735X-RAY DIFFRACTION99
4.3335-39.19260.16821270.15182791X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.4803 Å / Origin y: -7.5192 Å / Origin z: 91.5958 Å
111213212223313233
T0.165 Å20.0059 Å20.0051 Å2-0.1419 Å20.0024 Å2--0.2181 Å2
L-0.0304 °20.0433 °2-0.0299 °2-0.0593 °2-0.0146 °2--1.4644 °2
S-0.0165 Å °-0.0069 Å °0.0146 Å °0.0095 Å °0.025 Å °-0.0005 Å °-0.0046 Å °0.0197 Å °-0.0102 Å °
Refinement TLS groupSelection details: all

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