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- PDB-6nqv: Crystal structure of fast switching M159T mutant of fluorescent p... -

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Basic information

Entry
Database: PDB / ID: 6nqv
TitleCrystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2), Y63(3-CH3Y)
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / Dronpa2
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding
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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)27738 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: Science / Year: 2020
Title: Electrostatic control of photoisomerization pathways in proteins.
Authors: Romei, M.G. / Lin, C.Y. / Mathews, I.I. / Boxer, S.G.
History
DepositionJan 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)231,8058
Polymers231,8058
Non-polymers00
Water3,081171
1
A: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9024
Polymers115,9024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
2
F: Fluorescent protein Dronpa

D: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9024
Polymers115,9024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Unit cell
Length a, b, c (Å)79.988, 85.729, 143.006
Angle α, β, γ (deg.)90.00, 94.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fluorescent protein Dronpa


Mass: 28975.604 Da / Num. of mol.: 8 / Mutation: M159T, E218G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Tris-HCl at pH 7.4, 0.1 M MgCl2, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.7→39.344 Å / Num. obs: 51870 / % possible obs: 97.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.2 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3833 / CC1/2: 0.842 / Rrim(I) all: 1.38 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTS

4uts


Resolution: 2.7→39.344 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.71
RfactorNum. reflection% reflection
Rfree0.2953 1962 3.8 %
Rwork0.2552 --
obs0.2567 51632 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13764 0 0 171 13935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914268
X-RAY DIFFRACTIONf_angle_d1.23619304
X-RAY DIFFRACTIONf_dihedral_angle_d8.16810363
X-RAY DIFFRACTIONf_chiral_restr0.0741974
X-RAY DIFFRACTIONf_plane_restr0.0092523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.38741340.36013593X-RAY DIFFRACTION98
2.7675-2.84230.37851130.33983576X-RAY DIFFRACTION98
2.8423-2.92590.39031680.34253548X-RAY DIFFRACTION98
2.9259-3.02030.36051360.32973527X-RAY DIFFRACTION98
3.0203-3.12820.34471410.30763541X-RAY DIFFRACTION98
3.1282-3.25340.3981420.30053595X-RAY DIFFRACTION98
3.2534-3.40140.30721430.26693539X-RAY DIFFRACTION98
3.4014-3.58060.28731400.24923557X-RAY DIFFRACTION97
3.5806-3.80480.28081390.24323303X-RAY DIFFRACTION90
3.8048-4.09830.28291350.22643577X-RAY DIFFRACTION98
4.0983-4.51020.25861530.20843592X-RAY DIFFRACTION98
4.5102-5.16160.24211340.20133586X-RAY DIFFRACTION98
5.1616-6.49830.26771500.23253614X-RAY DIFFRACTION98
6.4983-39.34810.24041340.2393522X-RAY DIFFRACTION93
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)
11.3406-0.43940.38870.8164-0.3011.0783-0.05880.21570.1069-0.07240.0304-0.0899-0.19090.26110.05771.2863-0.01740.06420.33980.01360.335726.832517.65357.4538
21.485-0.07720.28750.9774-0.02960.7098-0.1388-0.27920.0798-0.0380.14190.0521-0.277-0.35710.07640.88970.04070.07020.0629-0.05880.287247.0491-22.164313.6685
31.49240.05250.11741.59020.28031.44580.15890.253-0.0369-0.1176-0.1889-0.19510.0460.23670.03051.19890.05820.08420.45690.04230.347468.0129-39.609853.9254
41.64280.14320.25051.36790.21111.32310.0675-0.22660.07660.073-0.08320.09450.0173-0.1856-0.03650.6107-0.07450.06450.2248-0.03180.253685.95235.922717.4439
51.0262-0.1478-0.27990.7040.10021.4690.05360.1498-0.00220.0489-0.08020.1095-0.0027-0.11120.04521.19310.02580.03090.4556-0.070.297239.7873-26.935153.6947
61.05530.3053-0.08391.62360.35581.50760.119-0.16550.0760.0126-0.0938-0.1321-0.17290.2318-0.06550.5721-0.06960.04050.22950.01040.218834.04419.031717.5164
71.5358-0.1978-0.10441.1382-0.04981.3135-0.19290.0643-0.09930.05080.17320.3110.3717-0.1660.04691.2393-0.0164-0.00790.3102-0.02960.334280.81381.270257.5271
81.49350.4212-0.48711.3554-0.12420.9598-0.0454-0.2486-0.16380.2210.0118-0.24610.10750.3115-0.0230.87570.067-0.0030.22290.02670.291272.9055-38.854913.7729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 220)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 220)
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 220)
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 220)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 220)
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 220)
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 220)
8X-RAY DIFFRACTION8(chain 'H' and resid 2 through 220)

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