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- PDB-3svn: Crystal structure of mKate S158A mutant at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3svn
TitleCrystal structure of mKate S158A mutant at pH 7.5
ComponentsmKate
KeywordsFLUORESCENT PROTEIN / Fluoresent protein / pH sensor
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesArtificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsWang, Q. / Byrnes, L. / Sondermann, H.
CitationJournal: Plos One / Year: 2011
Title: Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant.
Authors: Wang, Q. / Byrnes, L.J. / Shui, B. / Rohrig, U.F. / Singh, A. / Chudakov, D.M. / Lukyanov, S. / Zipfel, W.R. / Kotlikoff, M.I. / Sondermann, H.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mKate
B: mKate
C: mKate
D: mKate


Theoretical massNumber of molelcules
Total (without water)104,9924
Polymers104,9924
Non-polymers00
Water14,682815
1
A: mKate


Theoretical massNumber of molelcules
Total (without water)26,2481
Polymers26,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mKate


Theoretical massNumber of molelcules
Total (without water)26,2481
Polymers26,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mKate


Theoretical massNumber of molelcules
Total (without water)26,2481
Polymers26,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mKate


Theoretical massNumber of molelcules
Total (without water)26,2481
Polymers26,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-47 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.328, 161.328, 76.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
mKate


Mass: 26247.992 Da / Num. of mol.: 4 / Mutation: S158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE WAS ENGINEERED USING THE PROTEIN SEQUENCE FP480 FROM ENTACMAEA QUADRICOLOR (UNP ...THIS SEQUENCE WAS ENGINEERED USING THE PROTEIN SEQUENCE FP480 FROM ENTACMAEA QUADRICOLOR (UNP D0VX33) AS THE ORIGINAL TEMPLATE

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl, 0.25M ammonium citrate dibasic, 22% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 11, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.99 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.899→43.933 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 3795 5.02 %
Rwork0.1718 --
obs0.1742 75527 97.8 %
all-73698 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.985 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4349 Å2-0 Å20 Å2
2---0.4349 Å20 Å2
3---0.8699 Å2
Refinement stepCycle: LAST / Resolution: 1.899→43.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7211 0 0 815 8026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077427
X-RAY DIFFRACTIONf_angle_d1.09810014
X-RAY DIFFRACTIONf_dihedral_angle_d15.4352804
X-RAY DIFFRACTIONf_chiral_restr0.0711069
X-RAY DIFFRACTIONf_plane_restr0.0051285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8989-1.92290.34311160.29712073X-RAY DIFFRACTION78
1.9229-1.94820.28141280.26112284X-RAY DIFFRACTION84
1.9482-1.97490.28571270.23432432X-RAY DIFFRACTION91
1.9749-2.00310.30621290.22332564X-RAY DIFFRACTION94
2.0031-2.0330.25231330.21822617X-RAY DIFFRACTION97
2.033-2.06480.27261510.20172648X-RAY DIFFRACTION98
2.0648-2.09870.25191550.1952690X-RAY DIFFRACTION100
2.0987-2.13480.21221230.17952712X-RAY DIFFRACTION100
2.1348-2.17370.24561410.18662694X-RAY DIFFRACTION100
2.1737-2.21550.24321350.18532709X-RAY DIFFRACTION100
2.2155-2.26070.24041400.18392722X-RAY DIFFRACTION100
2.2607-2.30980.27641490.1742729X-RAY DIFFRACTION100
2.3098-2.36360.22991420.18222673X-RAY DIFFRACTION100
2.3636-2.42270.23461270.17252708X-RAY DIFFRACTION100
2.4227-2.48820.26261470.1812730X-RAY DIFFRACTION100
2.4882-2.56140.25151400.18672732X-RAY DIFFRACTION100
2.5614-2.6440.24921510.18062669X-RAY DIFFRACTION100
2.644-2.73850.21031430.16792778X-RAY DIFFRACTION100
2.7385-2.84820.23661490.17862668X-RAY DIFFRACTION100
2.8482-2.97780.25081600.18642682X-RAY DIFFRACTION100
2.9778-3.13470.23681480.17832706X-RAY DIFFRACTION100
3.1347-3.3310.22371340.17052745X-RAY DIFFRACTION100
3.331-3.58810.19251500.16082732X-RAY DIFFRACTION100
3.5881-3.9490.20091330.152734X-RAY DIFFRACTION100
3.949-4.51990.15581560.12572723X-RAY DIFFRACTION100
4.5199-5.69270.16531520.12572761X-RAY DIFFRACTION100
5.6927-43.94510.21841360.19492817X-RAY DIFFRACTION100

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