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- PDB-5wj2: Crystal structure of the green fluorescent protein Clover -

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Basic information

Entry
Database: PDB / ID: 5wj2
TitleCrystal structure of the green fluorescent protein Clover
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / clover / GFP / 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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.409 Å
AuthorsLiu, C. / Campbell, B.C. / Petsko, G.A.
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of Green Fluorescent Protein Clover and Design of Clover-Based Redox Sensors.
Authors: Campbell, B.C. / Petsko, G.A. / Liu, C.F.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2018Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 4, 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)58,4472
Polymers58,4472
Non-polymers00
Water1,58588
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,2241
Polymers29,2241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,2241
Polymers29,2241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.063, 135.176, 168.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-305-

HOH

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Components

#1: Protein Green fluorescent protein /


Mass: 29223.703 Da / Num. of mol.: 2
Mutation: S30R, Y39N, S66X, Y66X, G66X, Q69A, F99S, N105T, Y145F, M153T, V163A, I171V, and T203H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.8 Å3/Da / Density % sol: 56.05 % / Mosaicity: 0.451 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 100mM Tris, pH 8.5, 50mM MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23899 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.47 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.045 / Rrim(I) all: 0.124 / Χ2: 1.033 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.447.40.8430.8470.3330.9071.046100
2.44-2.497.50.7280.8650.2870.7841.067100
2.49-2.537.50.640.9130.2520.6881.038100
2.53-2.597.50.6040.9030.2380.6491.06100
2.59-2.647.50.5090.9390.20.5481.074100
2.64-2.77.50.6830.1810.2650.7331.152100
2.7-2.777.50.3490.9670.1370.3751.021100
2.77-2.857.50.2950.9660.1160.3170.991100
2.85-2.937.50.2350.980.0920.2531.04100
2.93-3.027.50.1850.9870.0730.1991.019100
3.02-3.137.50.1370.9920.0540.1470.996100
3.13-3.267.50.1150.9930.0450.1231.013100
3.26-3.417.50.1040.9970.040.1111.024100
3.41-3.587.40.1420.9820.0550.1521.08100
3.58-3.817.40.1270.8790.050.1370.92100
3.81-4.17.40.1050.9550.0410.1131.059100
4.1-4.527.20.0550.9970.0220.0591.052100
4.52-5.177.30.0490.9980.0190.0530.99100
5.17-6.517.20.0540.9970.0220.0581.004100
6.51-506.80.0490.9980.020.0531.0199.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QYQ

1qyq


Resolution: 2.409→42.147 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1161 4.86 %Random
Rwork0.193 ---
obs0.1943 23883 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.409→42.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 0 88 3768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073769
X-RAY DIFFRACTIONf_angle_d0.9315086
X-RAY DIFFRACTIONf_dihedral_angle_d22.4031375
X-RAY DIFFRACTIONf_chiral_restr0.048544
X-RAY DIFFRACTIONf_plane_restr0.004665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4087-2.51830.2651350.2412740X-RAY DIFFRACTION97
2.5183-2.65110.28191480.23872803X-RAY DIFFRACTION100
2.6511-2.81710.26521410.24492794X-RAY DIFFRACTION100
2.8171-3.03460.25691490.23912804X-RAY DIFFRACTION100
3.0346-3.33990.23431380.19362843X-RAY DIFFRACTION100
3.3399-3.82290.20141590.18452855X-RAY DIFFRACTION100
3.8229-4.81530.17441430.1512876X-RAY DIFFRACTION100
4.8153-42.15370.20891480.19033007X-RAY DIFFRACTION100

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