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

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Basic information

Entry
Database: PDB / ID: 6nqs
TitleCrystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)- Y63(3-OMeY)
ComponentsFluorescent protein DronpaFluorescence
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: 2.5 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 21, 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / 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 / _pdbx_validate_close_contact.auth_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)231,9338
Polymers231,9338
Non-polymers00
Water10,863603
1
A: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9664
Polymers115,9664
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
2
F: Fluorescent protein Dronpa

D: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9664
Polymers115,9664
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
Unit cell
Length a, b, c (Å)82.396, 86.489, 144.082
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fluorescent protein Dronpa / Fluorescence


Mass: 28991.604 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 / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
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, 16% 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: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.5→39.866 Å / Num. obs: 69116 / % possible obs: 98.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.139 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5144 / CC1/2: 0.874 / Rrim(I) all: 1.12 / % possible all: 99.6

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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
Resolution: 2.5→39.87 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.1
RfactorNum. reflection% reflection
Rfree0.251 1996 2.91 %
Rwork0.214 --
obs0.215 68618 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13991 0 0 603 14594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714851
X-RAY DIFFRACTIONf_angle_d1.36420103
X-RAY DIFFRACTIONf_dihedral_angle_d6.53812133
X-RAY DIFFRACTIONf_chiral_restr0.0712046
X-RAY DIFFRACTIONf_plane_restr0.0072639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.34841500.2994777X-RAY DIFFRACTION99
2.5625-2.63180.33071290.28274764X-RAY DIFFRACTION99
2.6318-2.70920.32111550.26454801X-RAY DIFFRACTION99
2.7092-2.79660.33891350.25734759X-RAY DIFFRACTION99
2.7966-2.89660.29971410.274775X-RAY DIFFRACTION99
2.8966-3.01250.28441540.25724722X-RAY DIFFRACTION98
3.0125-3.14960.27421360.24514675X-RAY DIFFRACTION96
3.1496-3.31550.27111460.22554817X-RAY DIFFRACTION99
3.3155-3.52310.25551400.21264752X-RAY DIFFRACTION99
3.5231-3.7950.25031370.22974539X-RAY DIFFRACTION93
3.795-4.17650.23621410.19584752X-RAY DIFFRACTION98
4.1765-4.780.20621430.16094784X-RAY DIFFRACTION97
4.78-6.0190.17381440.16194867X-RAY DIFFRACTION100
6.019-39.87110.22081450.19194838X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.26851.49010.44513.0821.46282.74320.095-0.47370.6868-0.2365-0.40990.4777-0.09190.09530.28910.5592-0.00230.02950.32730.00930.458235.9924-0.714226.2366
20.774-0.0994-0.15160.58960.14421.09610.0806-0.0974-0.11130.2417-0.1253-0.0618-0.03530.04490.07910.5071-0.02050.05710.32760.01830.418733.8887-3.38217.8227
33.8309-3.4484-0.30343.20320.63871.1029-0.15910.3930.0612-0.20830.03120.174-0.2437-0.1670.20880.58350.01360.02140.34380.02560.548132.365-3.81716.9014
42.8622-2.5718-1.94487.66353.613.5589-0.01430.2647-0.0995-0.22690.045-0.33380.1718-0.0568-0.04170.57870.04540.04950.38980.0110.467831.6076-7.07078.3654
50.3716-0.70050.27361.9497-1.20271.41420.0738-0.04490.1166-0.151-0.0333-0.04550.13210.1479-0.09840.5104-0.03720.01310.3657-0.02910.511839.8595-1.327715.0513
64.71740.62220.40410.0740.05290.02670.3249-0.9319-0.30770.4077-0.048-0.5584-0.73540.0855-0.27520.8809-0.3106-0.02690.9317-0.03840.929251.783211.3053-0.4011
72.49870.3930.32731.1798-0.56862.53640.35810.28170.5676-0.6375-0.1707-0.0061-0.10640.1049-0.3480.3513-0.0202-0.02410.27390.04940.411640.0498-40.769245.5984
81.5503-0.8783-0.30063.19680.41861.42290.12460.12480.2316-0.5821-0.12820.0247-0.0776-0.28990.0410.2959-0.0124-0.07060.33440.02620.285837.0139-45.441546.7554
90.7137-0.1724-0.25661.83140.40511.0040.02310.03640.0522-0.2083-0.12140.0387-0.0255-0.15370.13790.287-0.0015-0.01820.31120.00490.344843.4879-43.213355.7881
103.36012.7709-1.34352.8829-1.86631.7040.0073-0.05460.13030.34230.05610.30710.07170.0396-0.03290.3326-0.01170.00990.2791-0.05670.342844.1767-45.93864.0702
111.02440.22580.81472.78730.92661.57730.07330.24090.12580.10230.09740.17370.294-0.1115-0.15160.2491-0.00620.01080.32030.05130.359136.2544-41.405756.8047
121.7025-0.2852-0.44470.1128-0.06880.42860.47681.0480.0455-0.33370.1662-0.28410.06720.0795-0.11380.61020.2654-0.06250.6777-0.07650.86924.5747-28.685972.1018
135.5941-0.4240.27831.59780.0221.6343-0.2314-0.00830.5670.37580.2362-0.2894-0.25650.22710.04580.7027-0.08380.05030.42150.05850.550578.2125-57.928824.3822
140.8102-0.1747-0.07391.4237-0.13021.1585-0.1188-0.02940.02440.04240.0141-0.017-0.01850.03760.13040.47790.00290.02140.34410.01210.433374.1572-58.183416.0366
152.30420.54790.36932.46050.31941.1603-0.06650.10330.3389-0.0484-0.01660.529-0.07240.04610.14860.4232-0.00160.09630.35460.00890.466474.9716-54.33017.1177
161.49081.069-0.57741.9317-1.90762.3290.1352-0.2674-0.2251-0.3807-0.1937-0.37880.29760.5170.11550.52820.05160.01810.3188-0.07670.605878.9309-65.955812.3727
175.4565-0.14190.65641.9082-0.38512.7252-0.39040.12310.2171-0.14030.01420.4573-0.1946-0.65720.32450.58190.0127-0.0950.4572-0.08420.501580.85-11.866347.3774
181.516-0.3747-0.38071.63230.27121.2719-0.07530.1505-0.1026-0.0495-0.05050.190.1063-0.09370.06680.2599-0.0132-0.02390.25660.00540.337183.4524-12.701458.1303
197.3306-0.5039-1.05711.68890.03912.4655-0.4118-0.2647-0.60460.19450.11270.52810.1454-0.21690.28690.67970.0150.14060.3538-0.01740.483545.504-44.945824.4852
201.00330.00810.71831.30530.33260.78510.0293-0.08050.0648-0.0065-0.05260.0332-0.0169-0.05720.03480.484-0.00840.07740.3230.00760.437648.8288-44.789813.8541
210.8948-0.7701-0.80773.64141.91612.5996-0.0329-0.16360.3274-0.2387-0.29450.0723-0.3744-0.71760.41370.62110.05680.1040.38040.07430.537643.3029-36.943411.8992
222.83010.3941-1.51782.02940.3163.10830.0602-0.277-0.7678-0.3765-0.0673-0.32810.19560.33730.00620.53030.091-0.01880.37020.10710.456230.51991.388547.2921
230.9110.10120.12231.1640.14770.9417-0.11780.1191-0.0007-0.0303-0.0028-0.1225-0.07570.01650.08810.29960.00110.02760.28570.01460.349126.3361.97354.2429
241.1912-1.62280.61235.2022-0.85840.3204-0.0936-0.0648-0.13060.17250.20870.22690.083-0.2179-0.09270.3033-0.0257-0.00340.2567-0.00260.349127.4230.525266.2952
251.225-0.27870.22712.1813-0.40511.38290.05980.05180.1470.054-0.0752-0.2525-0.1120.18350.02420.2696-0.00650.02780.2652-0.00870.378430.07763.920261.2241
261.99840.99880.47861.2244-0.50461.58040.4867-0.6530.02380.5417-0.50580.0174-0.04570.164-0.04030.51840.00320.0940.3997-0.01590.516287.6605-15.364626.128
270.42-0.20440.36940.7029-0.00940.91870.0435-0.08340.05450.1817-0.1038-0.01130.0051-0.0220.0640.484-0.04290.08350.3731-0.00240.459389.6824-12.815617.8091
283.56-3.34441.79143.3981-2.20592.03020.15780.4445-0.1579-0.2358-0.19920.5585-0.26820.10930.13490.59410.05130.07040.3451-0.05310.498791.5865-10.48387.762
291.2457-0.8225-0.29181.73880.42131.06680.0488-0.0525-0.08250.1482-0.0920.2433-0.1094-0.270.01570.5899-0.05190.10320.39930.04790.512383.6028-14.893615.0572
300.54860.27590.12990.14210.06950.01920.333-0.70440.0730.7164-0.25260.6055-0.1938-0.03540.07630.8877-0.24690.14031.06620.00561.007571.9152-27.5661-0.2249
313.5453-1.10310.03732.37611.35542.48030.27760.3764-0.46470.0576-0.35060.0220.3052-0.0836-0.02130.5187-0.00940.09810.4642-0.05630.507970.9628-56.284745.5242
321.1743-0.1436-0.39321.4629-0.06811.11750.02950.04870.1212-0.2974-0.0958-0.16140.0380.00680.02310.29790.00930.02280.26460.02230.339568.7461-53.296453.9323
332.61812.7181.40468.96272.29811.70.1723-0.4096-0.09690.5313-0.3808-0.2874-0.0484-0.240.10920.33040.00740.04390.26850.0270.321366.8769-50.798763.9952
341.04110.09580.00051.6964-0.2430.69830.01060.08550.2302-0.12580.0156-0.1562-0.01650.2108-0.07310.2908-0.00140.08180.30820.00660.471874.8524-55.444456.6943
353.8598-1.14250.51750.3302-0.15840.0557-0.01860.81140.033-0.0412-0.03190.52870.1970.5455-0.26360.72660.15480.210.72320.09620.99986.4872-67.92572.1845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 20 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 21 THROUGH 151 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 152 THROUGH 163 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 164 THROUGH 179 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 180 THROUGH 216 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 217 THROUGH 228 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 3 THROUGH 20 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 21 THROUGH 46 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 47 THROUGH 151 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 152 THROUGH 179 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 180 THROUGH 216 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 217 THROUGH 228 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 5 THROUGH 20 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 21 THROUGH 151 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 152 THROUGH 188 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 189 THROUGH 220 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 5 THROUGH 20 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 21 THROUGH 221 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 3 THROUGH 20 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 21 THROUGH 200 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 201 THROUGH 220 )
22X-RAY DIFFRACTION22CHAIN 'F' AND (RESID 23
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 21 THROUGH 135 )
24X-RAY DIFFRACTION24CHAIN 'F' AND (RESID 136 THROUGH 163 )
25X-RAY DIFFRACTION25CHAIN 'F' AND (RESID 164 THROUGH 220 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 3 THROUGH 20 )
27X-RAY DIFFRACTION27CHAIN 'G' AND (RESID 21 THROUGH 151 )
28X-RAY DIFFRACTION28CHAIN 'G' AND (RESID 152 THROUGH 179 )
29X-RAY DIFFRACTION29CHAIN 'G' AND (RESID 180 THROUGH 216 )
30X-RAY DIFFRACTION30CHAIN 'G' AND (RESID 217 THROUGH 228 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 3 THROUGH 20 )
32X-RAY DIFFRACTION32CHAIN 'H' AND (RESID 21 THROUGH 151 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 152 THROUGH 179 )
34X-RAY DIFFRACTION34CHAIN 'H' AND (RESID 180 THROUGH 216 )
35X-RAY DIFFRACTION35CHAIN 'H' AND (RESID 217 THROUGH 228 )

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