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- PDB-3bxa: Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 4.2 -

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Basic information

Entry
Database: PDB / ID: 3bxa
TitleMonomeric Far-red Fluorescent Protein mKate Crystallized at pH 4.2
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 / Resolution: 1.75 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: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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 / 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

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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)55,4733
Polymers55,2812
Non-polymers1921
Water5,441302
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
MethodPQS
2
B: Far-red fluorescent protein mKate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8332
Polymers27,6401
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-16 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.181, 98.181, 106.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

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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) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 17.5% w/v PEG 3350, 0.07M citric acid, pH 4.2, 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: 1.75→30 Å / Num. obs: 50567 / % possible obs: 99.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.041 / Χ2: 0.943 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.817.60.52250000.817199.1
1.81-1.897.60.35750220.847199.3
1.89-1.977.70.22450130.906199.3
1.97-2.077.70.1550630.998199.7
2.07-2.27.70.11450231.031199.7
2.2-2.377.70.08250871.009199.7
2.37-2.617.70.05850381.044199.9
2.61-2.997.70.04850750.986199.9
2.99-3.777.70.02851080.9331100
3.77-307.70.0251380.856199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.75→29.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.676 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1032 2.1 %RANDOM
Rwork0.18 ---
obs0.182 48843 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 13 302 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223818
X-RAY DIFFRACTIONr_angle_refined_deg1.7662.0325178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13424.132167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67415659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2971520
X-RAY DIFFRACTIONr_chiral_restr0.110.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022950
X-RAY DIFFRACTIONr_nbd_refined0.2140.21901
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.220
X-RAY DIFFRACTIONr_mcbond_it1.0131.52352
X-RAY DIFFRACTIONr_mcangle_it1.59723713
X-RAY DIFFRACTIONr_scbond_it2.43131696
X-RAY DIFFRACTIONr_scangle_it3.544.51465
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 61 -
Rwork0.261 3617 -
all-3678 -
obs--99.3 %

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