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- PDB-3svu: Crystal structure of mKate mutant S143C -

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Basic information

Entry
Database: PDB / ID: 3svu
TitleCrystal structure of mKate mutant S143C
Componentsmkate S143C
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesArtificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.695 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mkate S143C
B: mkate S143C
C: mkate S143C
D: mkate S143C


Theoretical massNumber of molelcules
Total (without water)105,1204
Polymers105,1204
Non-polymers00
Water90150
1
A: mkate S143C


Theoretical massNumber of molelcules
Total (without water)26,2801
Polymers26,2801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mkate S143C


Theoretical massNumber of molelcules
Total (without water)26,2801
Polymers26,2801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mkate S143C


Theoretical massNumber of molelcules
Total (without water)26,2801
Polymers26,2801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mkate S143C


Theoretical massNumber of molelcules
Total (without water)26,2801
Polymers26,2801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: mkate S143C
B: mkate S143C


Theoretical massNumber of molelcules
Total (without water)52,5602
Polymers52,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-17 kcal/mol
Surface area18120 Å2
MethodPISA
6
C: mkate S143C
D: mkate S143C


Theoretical massNumber of molelcules
Total (without water)52,5602
Polymers52,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-18 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.621, 161.621, 76.507
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 S143C


Mass: 26280.057 Da / Num. of mol.: 4 / Mutation: S143C
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 / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M tris-HCl, 0.1M ammonium citrate dibasic , 18% PEG3350, pH 7.4, 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: Sep 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: 2.7→50 Å / Num. all: 26725 / Num. obs: 26725 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.78 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementResolution: 2.695→44.049 Å / SU ML: 0.72 / σ(F): 0.15 / Phase error: 27.45 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2695 1988 8.41 %
Rwork0.1888 --
obs0.1955 23632 86.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.718 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.2625 Å2-0 Å20 Å2
2---10.2625 Å2-0 Å2
3---20.5249 Å2
Refinement stepCycle: LAST / Resolution: 2.695→44.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7194 0 0 50 7244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087415
X-RAY DIFFRACTIONf_angle_d1.2289997
X-RAY DIFFRACTIONf_dihedral_angle_d17.0552793
X-RAY DIFFRACTIONf_chiral_restr0.0761061
X-RAY DIFFRACTIONf_plane_restr0.0061283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6947-2.76210.41221040.29781117X-RAY DIFFRACTION63
2.7621-2.83680.40751110.26651240X-RAY DIFFRACTION68
2.8368-2.92030.3851180.24451340X-RAY DIFFRACTION76
2.9203-3.01450.34791310.24241442X-RAY DIFFRACTION80
3.0145-3.12220.2961300.24291417X-RAY DIFFRACTION80
3.1222-3.24720.32761350.24681545X-RAY DIFFRACTION86
3.2472-3.39490.34881450.2361581X-RAY DIFFRACTION89
3.3949-3.57380.31511520.21111634X-RAY DIFFRACTION91
3.5738-3.79760.29431580.18191676X-RAY DIFFRACTION93
3.7976-4.09060.21391570.15921661X-RAY DIFFRACTION93
4.0906-4.50190.23071540.14481702X-RAY DIFFRACTION94
4.5019-5.15250.20841580.13251706X-RAY DIFFRACTION96
5.1525-6.48830.22091700.1541757X-RAY DIFFRACTION97
6.4883-44.05450.20611650.17631826X-RAY DIFFRACTION98

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