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- PDB-4he4: Crystal structure of the yellow fluorescent protein phiYFP (Phial... -

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Basic information

Entry
Database: PDB / ID: 4he4
TitleCrystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)
ComponentsYellow fluorescent protein
KeywordsFLUORESCENT PROTEIN / phiYFP / yellow fluorescent protein / mutant variant of phiYFP / Thr-Tyr-Gly chromophore / beta-barrel / Biomarker / Thr-Tyr-Gly bicyclic chromophore
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
Yellow fluorescent protein
Similarity search - Component
Biological speciesPhialidium sp. SL-2003 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPletneva, N. / Pletnev, S. / Pletnev, V.Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis.
Authors: Pletneva, N.V. / Pletnev, V.Z. / Souslova, E. / Chudakov, D.M. / Lukyanov, S. / Martynov, V.I. / Arhipova, S. / Artemyev, I. / Wlodawer, A. / Dauter, Z. / Pletnev, S.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Yellow fluorescent protein
B: Yellow fluorescent protein


Theoretical massNumber of molelcules
Total (without water)54,2172
Polymers54,2172
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-15 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.870, 102.870, 242.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

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Components

#1: Protein Yellow fluorescent protein


Mass: 27108.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phialidium sp. SL-2003 (invertebrata) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RYS7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHOR STATES THAT THE REPORTED PROTEIN IS A MUTANT OF OF THE WILD TYPE PHIYFP. NCBI DATABASE: ...AUTHOR STATES THAT THE REPORTED PROTEIN IS A MUTANT OF OF THE WILD TYPE PHIYFP. NCBI DATABASE: ACCESSION CODE AY485333.1. THE COMPLETE SEQEUNCE IS SSGALLFHGKIPYVVEMEGNVDGHTFSIRGKGYGDASVGKVDAQFICTTGDVPVPWSTLV TTLTYGAQCFAKYGPELKDFYKSCMPEGYVQERTITFEGDGVFKTRAEVTFENGSVYNRV KLNGQGFKKDGHVLGKNLEFNFTPHCLYIWGDQANHGLKSAFKIMHEITGSKEDFIVADH TQMNTPIGGGPVHVPEYHHITYHVTLSKDVTDHRDNMSLVETVRAVDCRKTY

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.16 M NaH2PO4 x 2H2O, 16% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 31372 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.078 / Χ2: 1.132 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.127.10.56230330.946198.2
2.12-2.217.60.44430920.997199.5
2.21-2.317.80.31930901.081199.9
2.31-2.437.80.24231191.1691100
2.43-2.587.80.19231371.1651100
2.58-2.787.80.14431261.2411100
2.78-3.067.80.10931381.2011100
3.06-3.57.80.08231451.1851100
3.5-4.417.70.06731931.1621100
4.41-307.40.04432991.146199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QY3

1qy3


Resolution: 2.05→28.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.2092 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8031 / SU B: 5.374 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2085 / SU Rfree: 0.1895 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1581 5 %RANDOM
Rwork0.1958 ---
obs0.1989 31367 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.52 Å2 / Biso mean: 41.3494 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 0 181 3831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213763
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9445093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07224.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88515608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6161514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212914
X-RAY DIFFRACTIONr_mcbond_it1.1211.52291
X-RAY DIFFRACTIONr_mcangle_it1.98323691
X-RAY DIFFRACTIONr_scbond_it3.0931472
X-RAY DIFFRACTIONr_scangle_it4.6234.51401
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 113 -
Rwork0.278 2106 -
all-2219 -
obs--97.62 %

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