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- PDB-3ug0: Crystal structure of a Trp-less green fluorescent protein transla... -

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Basic information

Entry
Database: PDB / ID: 3ug0
TitleCrystal structure of a Trp-less green fluorescent protein translated by the simplified genetic code
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GREEN FLUORESCENT PROTEIN
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: 2.093 Å
AuthorsKawahara-Kobayashi, A. / Araiso, Y. / Matsuda, T. / Yokoyama, S. / Kigawa, T. / Nureki, O. / Kiga, D.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Simplification of the genetic code: restricted diversity of genetically encoded amino acids.
Authors: Kawahara-Kobayashi, A. / Masuda, A. / Araiso, Y. / Sakai, Y. / Kohda, A. / Uchiyama, M. / Asami, S. / Matsuda, T. / Ishitani, R. / Dohmae, N. / Yokoyama, S. / Kigawa, T. / Nureki, O. / Kiga, D.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Experimental preparation / Refinement description / Category: exptl_crystal_grow / software
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp ..._exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _software.language / _software.location / _software.name / _software.type / _software.version
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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,6271
Polymers25,6271
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.784, 63.050, 67.401
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: 25626.881 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-229
Mutation: T9A, W57F, Q80R, F99S, M153T, V163A, T200C, S205T, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Description: Escherichia coli BL21(DE3) / Gene: GFP / Plasmid: pGFP / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE SER65 IS MUTATED TO GLY. RESIDUES GLY65, TYR66 AND GLY67 CONSTITUTE THE CHROMOPHORE CRO.

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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: 2.15 Å3/Da / Density % sol: 42.7 % / Mosaicity: 0.411 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG 20000, 100mM MES (pH6.5), vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 13473 / % possible obs: 99.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 29.44 Å2 / Rmerge(I) obs: 0.11 / Χ2: 2.436 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.145.70.3876421.159197.7
2.14-2.186.20.3946521.202198.6
2.18-2.226.60.3886491.249199.7
2.22-2.267.10.3626791.313199.3
2.26-2.317.50.3366371.234199.5
2.31-2.377.70.3096701.34199.9
2.37-2.428.30.2886571.485199.8
2.42-2.498.60.2666691.436199.9
2.49-2.569.10.2336571.589199.8
2.56-2.659.20.2276781.732199.9
2.65-2.749.80.1896691.822199.6
2.74-2.8510.30.1756591.9091100
2.85-2.9810.30.1666712.134199.9
2.98-3.1411.20.1316662.681100
3.14-3.3311.50.126912.9861100
3.33-3.5911.80.1096783.613199.9
3.59-3.9511.70.0956913.8851100
3.95-4.5211.90.0826984.364199.7
4.52-5.712.50.0687043.3211100
5.7-5011.20.0657563.346199.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MEA

1mea


Resolution: 2.093→33.701 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.54 / σ(F): 1.46 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 665 4.95 %
Rwork0.1803 12772 -
obs0.1832 13437 99.36 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.459 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 83.83 Å2 / Biso mean: 33.6954 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.3675 Å20 Å20 Å2
2---0.0749 Å20 Å2
3---0.4424 Å2
Refinement stepCycle: LAST / Resolution: 2.093→33.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 0 74 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071842
X-RAY DIFFRACTIONf_angle_d1.3392505
X-RAY DIFFRACTIONf_chiral_restr0.074277
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d14.423675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0929-2.25440.31041420.24582453259597
2.2544-2.48120.25021340.192724992633100
2.4812-2.84010.28821130.190825542667100
2.8401-3.57760.23771310.179925712702100
3.5776-33.70490.20961450.159526952840100

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