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- PDB-2ogr: Crystal Structure of Yellow Fluorescent Protein from Zoanthus sp.... -

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Basic information

Entry
Database: PDB / ID: 2ogr
TitleCrystal Structure of Yellow Fluorescent Protein from Zoanthus sp. at 1.8 A Resolution
ComponentsFLUORESCENT PROTEIN FP538
KeywordsFLUORESCENT PROTEIN / GFP-like proteins / yellow fluorescent protein / Zoanthus sp. / chromophore structure / tetramer structure / intermonomer interfaces
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / GFP-like fluorescent chromoprotein FP538
Function and homology information
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletneva, N.V. / Pletnev, S.V. / Tikhonova, T.V. / Pletnev, V.Z.
CitationJournal: Bioorg.Khim.
Title: Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom
Authors: Pletneva, N.V. / Pletnev, S.V. / Chudakov, D.M. / Tikhonova, T.V. / Popov, V.O. / Martynov, V.I. / Wlodawer, A. / Dauter, Z. / Pletnev, V.Z.
History
DepositionJan 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLUORESCENT PROTEIN FP538
B: FLUORESCENT PROTEIN FP538
C: FLUORESCENT PROTEIN FP538
D: FLUORESCENT PROTEIN FP538


Theoretical massNumber of molelcules
Total (without water)104,6654
Polymers104,6654
Non-polymers00
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.343, 106.541, 115.674
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
FLUORESCENT PROTEIN FP538


Mass: 26166.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Plasmid: pQE30-zFP538 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: Q9U6Y4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085M HEPES, pH 7.5, 17% PEG 4000, 8.5% isopropanol, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 92110 / % possible obs: 91.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Χ2: 0.988 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.862.10.49153190.90653.1
1.86-1.942.70.40674010.93674.1
1.94-2.033.10.30488400.96488.3
2.03-2.133.40.26295741.00695.5
2.13-2.273.80.23399991.04899.5
2.27-2.444.10.176100331.05100
2.44-2.694.20.123100951.066100
2.69-3.084.20.074101140.98999.9
3.08-3.884.10.048101980.97499.8
3.88-3040.035105370.84299.7

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Phasing

Phasing MRRfactor: 0.442 / Cor.coef. Fo:Fc: 0.565
Highest resolutionLowest resolution
Rotation2.5 Å48.22 Å
Translation2.5 Å48.22 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.924 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 904 1 %RANDOM
Rwork0.184 ---
obs0.185 89843 89.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7188 0 0 497 7685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227385
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.969969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70724.444324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.568151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9481524
X-RAY DIFFRACTIONr_chiral_restr0.1490.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025644
X-RAY DIFFRACTIONr_nbd_refined0.2010.23179
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2509
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.25
X-RAY DIFFRACTIONr_mcbond_it1.1541.54594
X-RAY DIFFRACTIONr_mcangle_it1.84527164
X-RAY DIFFRACTIONr_scbond_it2.90433295
X-RAY DIFFRACTIONr_scangle_it4.4934.52805
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 44 -
Rwork0.299 3738 -
obs-3782 51.72 %

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