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- PDB-6mz3: mCherry pH sensitive mutant - M66T (mCherryTYG) -

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Basic information

Entry
Database: PDB / ID: 6mz3
TitlemCherry pH sensitive mutant - M66T (mCherryTYG)
ComponentsPAmCherry1 protein
KeywordsLUMINESCENT PROTEIN / Fluorescent protein / beta barrel / biosensor
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.088 Å
AuthorsHaynes, E.P. / Tantama, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Anal.Chem. / Year: 2019
Title: Quantifying Acute Fuel and Respiration Dependent pH Homeostasis in Live Cells Using the mCherryTYG Mutant as a Fluorescence Lifetime Sensor.
Authors: Haynes, E.P. / Rajendran, M. / Henning, C.K. / Mishra, A. / Lyon, A.M. / Tantama, M.
History
DepositionNov 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAmCherry1 protein


Theoretical massNumber of molelcules
Total (without water)30,5601
Polymers30,5601
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.806, 42.782, 61.067
Angle α, β, γ (deg.)90.00, 112.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PAmCherry1 protein


Mass: 30560.250 Da / Num. of mol.: 1 / Mutation: M66T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry, PAmCherry1 / Production host: Escherichia coli (E. coli) / References: UniProt: D1MPT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris-HCl, 100 mM NaOAc, 30% PEG 4000, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.088 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.088 Å / Relative weight: 1
ReflectionResolution: 1.088→19.979 Å / Num. obs: 76260 / % possible obs: 93.6 % / Redundancy: 6.8 % / Net I/σ(I): 10.4
Reflection shellResolution: 1.09→1.21 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
autoPROC1.0.5data collection
XDSdata reduction
Aimless0.5.31data scaling
PHENIXphasing
RefinementResolution: 1.088→19.979 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1776 2001 2.62 %
Rwork0.1668 --
obs0.1671 76260 78.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.088→19.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 0 313 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051917
X-RAY DIFFRACTIONf_angle_d0.9922611
X-RAY DIFFRACTIONf_dihedral_angle_d19.577753
X-RAY DIFFRACTIONf_chiral_restr0.096270
X-RAY DIFFRACTIONf_plane_restr0.006342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0882-1.11540.4214140.3148569X-RAY DIFFRACTION8
1.1154-1.14550.2933510.27751730X-RAY DIFFRACTION26
1.1455-1.17920.2736760.24812896X-RAY DIFFRACTION43
1.1792-1.21730.21851150.22214017X-RAY DIFFRACTION59
1.2173-1.26080.22391330.20265484X-RAY DIFFRACTION81
1.2608-1.31130.19431740.19156409X-RAY DIFFRACTION95
1.3113-1.37090.20681860.17886531X-RAY DIFFRACTION96
1.3709-1.44320.16811720.17266591X-RAY DIFFRACTION97
1.4432-1.53360.17991750.1686563X-RAY DIFFRACTION97
1.5336-1.65190.16511760.15966426X-RAY DIFFRACTION95
1.6519-1.81810.16441790.16336701X-RAY DIFFRACTION98
1.8181-2.08090.17431810.15386762X-RAY DIFFRACTION99
2.0809-2.62080.16431820.16596781X-RAY DIFFRACTION99
2.6208-19.98230.17551870.15816799X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21780.0323-0.20.48630.02880.2545-0.01260.03060.03760.04480.04510.0433-0.0459-0.00040.00240.10650.0105-0.00120.09420.00070.100836.731921.733620.5692
20.3955-0.0613-0.12820.2244-0.19820.268-0.00720.01490.0716-0.1099-0.03050.0615-0.2221-0.0813-0.00220.11370.0037-0.00010.0923-0.00540.09138.561824.81019.7622
30.1858-0.162-0.01770.1814-0.11530.2787-0.0293-0.0531-0.0274-0.0417-0.046-0.06320.01450.0514-0.17910.0816-0.00620.00640.0815-0.00290.07650.252216.41889.8648
40.14150.0304-0.08820.087-0.01560.3003-0.0048-0.0069-0.0017-0.0006-0.0081-0.0057-0.0118-0.032100.09510.00050.00290.0901-0.00390.09241.222714.21347.5988
50.2192-0.0099-0.13620.4337-0.1740.6073-0.0097-0.0220.00060.00450.0213-0.0094-0.0060.01280.00110.0770.00760.00030.0752-0.00630.076442.432515.082717.5701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 138 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 4 through 24 )
4X-RAY DIFFRACTION4chain 'A' and (resid 25 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 137 )

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