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- PDB-3bxb: Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 3bxb
TitleMonomeric Far-red Fluorescent Protein mKate Crystallized at pH 7.0
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
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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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
C: Far-red fluorescent protein mKate
D: Far-red fluorescent protein mKate
E: Far-red fluorescent protein mKate
F: Far-red fluorescent protein mKate
G: Far-red fluorescent protein mKate
H: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)221,1248
Polymers221,1248
Non-polymers00
Water6,323351
1
A: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Far-red fluorescent protein mKate


Theoretical massNumber of molelcules
Total (without water)27,6401
Polymers27,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.176, 104.967, 123.028
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Far-red fluorescent protein mKate


Mass: 27640.482 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% w/v PEG 6000, 1.0M LiCl, 0.1M HEPES, pH 7.0, 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: 2.6→30 Å / Num. obs: 55727 / % possible obs: 99.9 %
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.506 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementResolution: 2.6→29.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.087 / SU ML: 0.284 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.263 2814 5.05 %
Rwork0.17 --
obs-55727 99.7 %
Solvent computationBsol: 28.7 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 44.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.394 Å20 Å2-4.942 Å2
2--0.706 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14264 0 0 351 14615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.935
X-RAY DIFFRACTIONf_dihedral_angle_d13.204
X-RAY DIFFRACTIONf_chiral_restr0.066
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shellResolution: 2.6→2.61 Å
RfactorNum. reflection% reflection
Rwork0.224 497 -
obs--93 %

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