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- PDB-3h1r: Order-disorder structure of fluorescent protein FP480 -

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Basic information

Entry
Database: PDB / ID: 3h1r
TitleOrder-disorder structure of fluorescent protein FP480
ComponentsFluorescent protein FP480
KeywordsFLUORESCENT PROTEIN / OD-structure / order-disorder structure
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Fluorescent protein FP480
Function and homology information
Biological speciesEntacmaea Quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsPletnev, S. / Morozova, K.S. / Verkhusha, V.V. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Rotational order-disorder structure of fluorescent protein FP480
Authors: Pletnev, S. / Morozova, K.S. / Verkhusha, V.V. / Dauter, Z.
History
DepositionApr 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorescent protein FP480


Theoretical massNumber of molelcules
Total (without water)26,3371
Polymers26,3371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.394, 91.394, 53.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Fluorescent protein FP480


Mass: 26336.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea Quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX33*PLUS
Has protein modificationY

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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

Crystal growTemperature: 293 K / pH: 6.5
Details: 100mM Bis-Tris, 25% PEG 3350, 200mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / 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: 2.4→30 Å / Num. obs: 4611 / % possible obs: 99.9 %
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.695 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→28.9 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / Occupancy max: 0.49 / Occupancy min: 0.49 / SU B: 13.668 / SU ML: 0.333 / ESU R Free: 0.526 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES REFINED INDIVIDUALLY. THE COORDINATES REPRESENT THE CRYSTAL STRUCTURE OF FLUORESCENT PROTEIN FP480 SUFFERING FROM ROTATIONAL ORDER-DISORDER PATHOLOGY. THE LATTICE IS COMPOSED OF THE ...Details: U VALUES REFINED INDIVIDUALLY. THE COORDINATES REPRESENT THE CRYSTAL STRUCTURE OF FLUORESCENT PROTEIN FP480 SUFFERING FROM ROTATIONAL ORDER-DISORDER PATHOLOGY. THE LATTICE IS COMPOSED OF THE TETRAMERS WITH 222 SYMMETRY INCORPORATED INTO AN ARRAY IN TWO DIFFERENT ORIENTATIONS, ROTATED 90 DEGREES WITH RESPECT TO EACH OTHER AROUND THE CRYSTAL C-AXIS, WITH TETRAMER AXES COINCIDENT WITH CRYSTALLOGRAPHIC TWOFOLD AXES. THE DISTRIBUTION OF ALTERNATIVELY ORIENTED TETRAMERS IN THE CRYSTAL IS NEARLY RANDOM. THIS CREATES THE STRUCTURE WITH STATISTICALLY AVERAGED I422 SYMMETRY.
RfactorNum. reflection% reflection
Rfree0.321 441 9.6 %
Rwork0.228 --
obs0.236 4602 100 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.41→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 0 0 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221844
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.9872496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4755221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12924.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27715312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.649158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211414
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_it2.2231108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.75651789
X-RAY DIFFRACTIONr_scbond_it5.8796736
X-RAY DIFFRACTIONr_scangle_it7.748707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å
RfactorNum. reflection% reflection
Rfree0.38 35 -
Rwork0.244 283 -
obs--100 %

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