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- PDB-3svr: Crystal structure of mkate mutant S158A/S143C at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3svr
TitleCrystal structure of mkate mutant S158A/S143C at pH 7.5
Componentsmkate S158A/S143C
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 / SAD / Resolution: 1.907 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 S158A/S143C
B: mkate S158A/S143C
C: mkate S158A/S143C
D: mkate S158A/S143C


Theoretical massNumber of molelcules
Total (without water)105,0564
Polymers105,0564
Non-polymers00
Water13,781765
1
A: mkate S158A/S143C


Theoretical massNumber of molelcules
Total (without water)26,2641
Polymers26,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mkate S158A/S143C


Theoretical massNumber of molelcules
Total (without water)26,2641
Polymers26,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mkate S158A/S143C


Theoretical massNumber of molelcules
Total (without water)26,2641
Polymers26,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mkate S158A/S143C


Theoretical massNumber of molelcules
Total (without water)26,2641
Polymers26,2641
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 area12610 Å2
ΔGint-44 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.310, 161.310, 75.441
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 S158A/S143C


Mass: 26264.057 Da / Num. of mol.: 4 / Mutation: S158A/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


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl, 22% PEG3350, 0.1M MgCl2, 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 / Num. all: 73856 / Num. obs: 73856 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.96 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: SAD / Resolution: 1.907→40.327 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 3736 5.06 %
Rwork0.1797 --
obs0.1821 73785 97.7 %
all-73785 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.42 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.907→40.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 0 765 7933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077528
X-RAY DIFFRACTIONf_angle_d1.19810153
X-RAY DIFFRACTIONf_dihedral_angle_d17.8422867
X-RAY DIFFRACTIONf_chiral_restr0.0761069
X-RAY DIFFRACTIONf_plane_restr0.0061302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9069-1.9310.31111140.28252117X-RAY DIFFRACTION80
1.931-1.95640.30681050.25362302X-RAY DIFFRACTION87
1.9564-1.98320.28091380.24462371X-RAY DIFFRACTION89
1.9832-2.01160.29641160.23422432X-RAY DIFFRACTION93
2.0116-2.04160.28831190.22552572X-RAY DIFFRACTION95
2.0416-2.07350.28341380.21922548X-RAY DIFFRACTION97
2.0735-2.10750.25641420.20482591X-RAY DIFFRACTION98
2.1075-2.14380.29051520.19882648X-RAY DIFFRACTION100
2.1438-2.18280.26411450.19852618X-RAY DIFFRACTION100
2.1828-2.22480.26581310.1962658X-RAY DIFFRACTION100
2.2248-2.27020.25821390.19522635X-RAY DIFFRACTION100
2.2702-2.31960.24961380.1882651X-RAY DIFFRACTION100
2.3196-2.37350.26451340.1942655X-RAY DIFFRACTION100
2.3735-2.43290.24311480.18112651X-RAY DIFFRACTION100
2.4329-2.49860.21711330.19272637X-RAY DIFFRACTION100
2.4986-2.57210.27481320.19522659X-RAY DIFFRACTION100
2.5721-2.65510.2651510.19942661X-RAY DIFFRACTION100
2.6551-2.750.23541350.18552622X-RAY DIFFRACTION100
2.75-2.86010.26391440.19252675X-RAY DIFFRACTION100
2.8601-2.99020.2681600.19832624X-RAY DIFFRACTION100
2.9902-3.14780.27661390.19362667X-RAY DIFFRACTION100
3.1478-3.3450.22281480.17672663X-RAY DIFFRACTION100
3.345-3.60310.20331420.16372626X-RAY DIFFRACTION100
3.6031-3.96540.18731390.15552679X-RAY DIFFRACTION100
3.9654-4.53850.16871680.13332633X-RAY DIFFRACTION100
4.5385-5.71540.15881380.13592714X-RAY DIFFRACTION100
5.7154-40.33650.20941480.18462740X-RAY DIFFRACTION100

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