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- PDB-3ai5: Crystal structure of yeast enhanced green fluorescent protein-ubi... -

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Basic information

Entry
Database: PDB / ID: 3ai5
TitleCrystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein
Componentsyeast enhanced green fluorescent protein,Ubiquitin
KeywordsFluorescent Protein / transcription / green fluorescent protein / ubiquitin / fusion protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / ribosome / structural constituent of ribosome / translation / nucleus / cytoplasm
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Ribosomal L40e family / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Green Fluorescent Protein / Green fluorescent protein / Ribosomal L40e family / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
60S ribosomal protein L40 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSuzuki, N. / Wakatsuki, S. / Kawasaki, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Crystallization of small proteins assisted by green fluorescent protein
Authors: Suzuki, N. / Hiraki, M. / Yamada, Y. / Matsugaki, N. / Igarashi, N. / Kato, R. / Dikic, I. / Drew, D. / Iwata, S. / Wakatsuki, S. / Kawasaki, M.
History
DepositionMay 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _pdbx_entry_details.sequence_details / _struct_ref.db_code / _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 1.3Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: yeast enhanced green fluorescent protein,Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0626
Polymers34,7511
Non-polymers3105
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.515, 65.649, 70.225
Angle α, β, γ (deg.)90.00, 130.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein yeast enhanced green fluorescent protein,Ubiquitin


Mass: 34751.258 Da / Num. of mol.: 1
Fragment: residues 1-230 for yeast enhanced green fluorescent protein,residues 1-74 for Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Mus musculus (house mouse)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9Q9J0, UniProt: P42212*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Compound detailsYEAST ENHANCED GREEN FLUORESCENT PROTEIN - UBIQUITIN FUSION PROTEIN
Sequence detailsTHE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN HAS BEEN DEPOSITED IN GENBANK WITH ...THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN HAS BEEN DEPOSITED IN GENBANK WITH ACCESSION CODE, ABI82055. residues -2,-1,0 are expression tags, and residue 68 CR2 is CHROMOPHORE (GLY-TYR-GLY).

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1% Tryptone, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2009 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 62484 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.58 / Num. unique all: 3167 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREP10.2.35phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GFL

1gfl


Resolution: 1.4→27.1 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.905 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20873 3172 5.1 %RANDOM
Rwork0.1787 ---
obs0.18022 59297 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.04 Å2
2--0.01 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 20 299 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9733302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06625.517116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75715434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.438158
X-RAY DIFFRACTIONr_chiral_restr0.1380.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1591.51481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09222401
X-RAY DIFFRACTIONr_scbond_it3.0623971
X-RAY DIFFRACTIONr_scangle_it4.9554.5901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 221 -
Rwork0.266 4341 -
obs--98.43 %
Refinement TLS params.Method: refined / Origin x: 34.8061 Å / Origin y: 0.1033 Å / Origin z: 7.9771 Å
111213212223313233
T0.0052 Å20.0015 Å20.0067 Å2-0.0066 Å2-0.0026 Å2--0.032 Å2
L0.5006 °20.0398 °20.1568 °2-0.3389 °20.0753 °2--0.5658 °2
S0.0002 Å °-0.0106 Å °-0.0117 Å °-0.037 Å °-0.014 Å °-0.0115 Å °0.004 Å °0.0164 Å °0.0137 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 230
2X-RAY DIFFRACTION1A232 - 303

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