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- PDB-3bx9: Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 2.0 -

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Basic information

Entry
Database: PDB / ID: 3bx9
TitleMonomeric Far-red Fluorescent Protein mKate Crystallized at pH 2.0
ComponentsFar-red fluorescent protein mKate
KeywordsFLUORESCENT PROTEIN / Far-red fluorescent protein / E. quadricolor / Chromophore structure / pH-induced cis-trans izomerization
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / CITRIC ACID
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletnev, S. / Pletneva, N. / Pletnev, V.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A Crystallographic Study of Bright Far-Red Fluorescent Protein mKate Reveals pH-induced cis-trans Isomerization of the Chromophore.
Authors: Pletnev, S. / Shcherbo, D. / Chudakov, D.M. / Pletneva, N. / Merzlyak, E.M. / Wlodawer, A. / Dauter, Z. / Pletnev, V.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Far-red fluorescent protein mKate
B: Far-red fluorescent protein mKate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,61810
Polymers55,2812
Non-polymers1,3378
Water4,666259
1
A: Far-red fluorescent protein mKate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3095
Polymers27,6401
Non-polymers6684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Far-red fluorescent protein mKate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3095
Polymers27,6401
Non-polymers6684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Far-red fluorescent protein mKate
hetero molecules

A: Far-red fluorescent protein mKate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,61810
Polymers55,2812
Non-polymers1,3378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area6210 Å2
ΔGint-19 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.852, 67.852, 413.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Far-red fluorescent protein mKate


Mass: 27640.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / pH: 2
Details: 20% w/v PEG 3350, 0.2M ammonium citrate tribasic, 0.4M citric acid, pH 2.0, 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 Å
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→30.43 Å / Num. all: 53976 / Num. obs: 52642 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 5.63 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UIS

1uis


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.224 / SU ML: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.247 1150 2.2 %
Rwork0.205 --
obs0.205 52642 97.7 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 90 259 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7732.0195147
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1815456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23824.364165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91715652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9841518
X-RAY DIFFRACTIONr_chiral_restr0.1120.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022912
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21739
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22541
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.141.52341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69523664
X-RAY DIFFRACTIONr_scbond_it2.65731683
X-RAY DIFFRACTIONr_scangle_it3.9134.51483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.326 86 -
Rwork0.281 3739 -
obs--98.84 %

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