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- PDB-6xwy: Highly pH-resistant long stokes-shift, red fluorescent protein mC... -

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Basic information

Entry
Database: PDB / ID: 6xwy
TitleHighly pH-resistant long stokes-shift, red fluorescent protein mCRISPRed
ComponentsRed fluorescent protein eqFP611
KeywordsFLUORESCENT PROTEIN / pH resistant / long stokes shift / lss / red fluorescent protein
Function / homologyGreen fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / MALONIC ACID / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsErdogan, M. / Fabritius, A. / Basquin, J. / Griesbeck, O.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells.
Authors: Erdogan, M. / Fabritius, A. / Basquin, J. / Griesbeck, O.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Red fluorescent protein eqFP611
B: Red fluorescent protein eqFP611
C: Red fluorescent protein eqFP611
D: Red fluorescent protein eqFP611
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,76710
Polymers99,2684
Non-polymers4986
Water10,917606
1
A: Red fluorescent protein eqFP611
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0874
Polymers24,8171
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Red fluorescent protein eqFP611
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9833
Polymers24,8171
Non-polymers1662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)24,8171
Polymers24,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Red fluorescent protein eqFP611
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8792
Polymers24,8171
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.020, 96.861, 232.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Red fluorescent protein eqFP611 / GFP-like chromoprotein


Mass: 24817.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ISF8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Tris pH 8.0 0.2 M Ammonium Sulfate 26 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.43 Å / Num. obs: 202826 / % possible obs: 99.88 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 18.37
Reflection shellResolution: 1.75→1.812 Å / Num. unique obs: 10267 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0M
Resolution: 1.75→48.43 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 10156 5.01 %
Rwork0.2034 --
obs0.2048 202826 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 33 606 7559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077109
X-RAY DIFFRACTIONf_angle_d1.1399571
X-RAY DIFFRACTIONf_dihedral_angle_d11.574981
X-RAY DIFFRACTIONf_chiral_restr0.062996
X-RAY DIFFRACTIONf_plane_restr0.0071250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.40743390.37746438X-RAY DIFFRACTION100
1.77-1.790.37013350.35326401X-RAY DIFFRACTION100
1.79-1.810.34343400.31716417X-RAY DIFFRACTION100
1.81-1.840.30643330.29056421X-RAY DIFFRACTION100
1.84-1.860.29913420.27376452X-RAY DIFFRACTION100
1.86-1.890.29543340.26486384X-RAY DIFFRACTION100
1.89-1.910.2743420.24796478X-RAY DIFFRACTION100
1.91-1.940.25973390.24426350X-RAY DIFFRACTION100
1.94-1.970.2683470.24036498X-RAY DIFFRACTION100
1.97-20.28983420.2446403X-RAY DIFFRACTION100
2-2.040.29963350.23726397X-RAY DIFFRACTION100
2.04-2.070.25543390.2286416X-RAY DIFFRACTION100
2.07-2.110.27613320.22546415X-RAY DIFFRACTION100
2.11-2.160.25463430.21476461X-RAY DIFFRACTION100
2.16-2.20.26453370.21516383X-RAY DIFFRACTION100
2.2-2.260.24873370.21886411X-RAY DIFFRACTION100
2.26-2.310.27623390.21216523X-RAY DIFFRACTION100
2.31-2.380.27393340.2116368X-RAY DIFFRACTION100
2.38-2.440.25123390.26379X-RAY DIFFRACTION100
2.44-2.520.23443390.20296439X-RAY DIFFRACTION100
2.52-2.610.22993460.20026410X-RAY DIFFRACTION100
2.61-2.720.23833380.20696429X-RAY DIFFRACTION100
2.72-2.840.21693360.19736401X-RAY DIFFRACTION100
2.84-2.990.23013470.20266452X-RAY DIFFRACTION100
2.99-3.180.22823400.20216451X-RAY DIFFRACTION100
3.18-3.430.23243310.18986365X-RAY DIFFRACTION100
3.43-3.770.21193340.18796456X-RAY DIFFRACTION100
3.77-4.310.19843410.17666405X-RAY DIFFRACTION100
4.31-5.430.19373390.16246428X-RAY DIFFRACTION100
5.44-48.430.17353370.18866439X-RAY DIFFRACTION100
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)
12.0714-0.2919-0.10696.49525.08565.55090.18630.3204-0.16550.07240.364-0.85890.22390.1915-0.55370.20340.0573-0.02510.2968-0.08620.33524.6518-26.873212.2353
22.91882.64212.57565.53215.25843.93480.15030.0952-0.24910.1664-0.0547-0.0920.202-0.0236-0.21080.33930.0482-0.03370.2495-0.05320.18987.1263-24.754118.3914
31.97060.29631.32132.21291.39982.04570.08420.1429-0.24120.0140.0075-0.12090.0601-0.039-0.10110.25920.0362-0.00780.2483-0.05860.2518-1.7525-28.226913.4253
42.8125-0.7778-1.10923.46282.69865.49410.0107-0.03250.08130.06710.0205-0.1705-0.0861-0.0046-0.01240.16530.0293-0.01790.1715-0.03440.1478-1.915-17.300517.7357
55.4252-0.43544.81943.70550.99358.29250.12590.0636-0.13220.0249-0.06660.17640.10080.22160.03660.14180.01770.04340.1797-0.05740.1711-11.7443-24.165919.0929
63.3974-0.69594.08984.3864-2.53118.5820.1337-0.4244-0.05630.27090.22240.1748-0.2014-0.6953-0.48420.17480.00990.02010.218-0.06530.19-12.5168-22.539922.5444
75.4029-0.1706-3.2742.2796-0.23268.9856-0.09370.0911-0.048-0.06480.0205-0.2443-0.0022-0.76450.13640.25870.0221-0.00690.184-0.04110.1632-11.1987-19.32516.682
83.90584.30450.1866.52750.48280.0642-0.4461.6355-0.2058-1.46990.1179-0.3569-0.3701-0.2830.12070.50920.0982-0.10190.72220.02330.294-10.2999-24.898-3.6137
96.5070.31695.2151.96280.03125.59890.2154-0.6888-0.82920.37970.0665-0.07890.2564-0.5647-0.21610.23780.0436-0.04030.26250.02030.2793-5.2755-31.826621.8905
107.22594.80796.08026.13463.89827.8502-0.10630.14360.01810.22680.0729-0.1866-0.07250.19380.13840.25120.0103-0.01160.1526-0.01160.2322-1.9388-31.124221.1842
113.0891.06051.75727.94672.49792.9511-0.2457-0.15450.262-0.4265-0.14470.8869-0.4556-0.13210.38350.15420.00540.03680.2002-0.02190.1558-47.1242-17.519836.4537
122.87580.0780.34212.77621.17931.1144-0.1025-0.25660.01770.20350.0128-0.00330.0072-0.0090.09190.23280.0222-0.04460.1904-0.02680.2062-45.5651-19.843340.8688
132.540.2859-0.14318.7792-0.64361.8626-0.27380.0761-0.27940.00870.1992-0.03530.0223-0.07870.11140.17090.0114-0.03070.1899-0.0690.237-43.3394-29.751836.9424
145.85232.14860.00175.24260.23572.4631-0.1778-0.50840.06630.57540.11990.2180.1341-0.01650.04250.34110.1182-0.01730.2463-0.01030.217-40.4807-30.454748.8152
155.05094.7315-3.53048.3383-4.18453.506-0.1605-0.109-0.20490.35790.11810.05270.06610.00860.05470.31670.0575-0.00760.2453-0.00980.254-37.257-30.654444.1503
164.2414-0.07323.79170.91440.94644.4378-0.89120.18551.47430.17390.6459-0.6395-1.02761.51970.84260.43-0.0914-0.20190.4695-0.01720.6138-25.8638-13.432939.5291
175.53991.69145.42913.58951.21275.9481-0.252-1.3729-1.06380.89140.24860.20380.255-0.6340.07440.35510.05540.03010.2567-0.05780.2648-48.4269-23.068749.7563
189.67220.11456.53681.46671.22336.61390.0362-0.1812-0.39360.57080.10370.22930.50540.0572-0.17630.31980.1015-0.02490.2486-0.03650.2411-50.1767-22.148346.8364
196.61431.03731.10112.06450.82751.2089-0.5744-0.19340.6722-0.24270.07840.4166-0.3045-0.25130.49310.23340.0518-0.05030.222-0.04160.4612-29.5712.098122.7146
207.47953.38657.04164.35232.99428.36730.1917-0.36080.4511-0.1823-0.40870.24520.1211-0.37710.18690.21840.0139-0.05450.1634-0.05180.4406-25.05917.302123.4349
212.84720.35850.93493.05651.33180.8853-0.0030.15940.2435-0.2162-0.12550.2428-0.1055-0.08210.15740.24040.0189-0.04010.207-0.00610.301-28.1796-0.537616.7498
223.39491.1363-4.4373.2552-0.22975.897-0.04460.08540.15870.0138-0.0085-0.1981-0.01930.0712-0.03660.17020.0167-0.03470.1434-0.02590.2827-18.4544-4.736320.1781
233.42091.27490.41512.55040.72411.7590.01310.12850.4821-0.1544-0.0169-0.0957-0.08780.0606-0.03510.1830.0542-0.02980.14960.02130.3538-17.3704-0.269816.2905
247.51265.1986-2.70764.2852-4.03696.99290.17350.52630.9859-0.56230.01711.0498-0.05780.1831-0.21780.21740.040.0550.28490.0610.3395-15.5449-2.1498.2026
255.67746.3503-6.14437.4764-6.42798.284-0.10240.54710.1985-0.1410.1596-0.2942-0.0493-0.09040.07450.21080.0533-0.01330.26650.01830.3564-16.7545-6.663213.1511
262.2297-0.4943-0.0524.64961.54782.36240.05620.14450.2843-0.3846-0.25710.3149-0.032-0.15020.20360.15540.0256-0.08030.2409-0.02760.3417-27.5103-1.088112.7669
273.32780.41492.47662.01081.98564.08940.1080.0153-0.2760.21740.2659-0.16190.22980.393-0.36710.2650.0713-0.06380.2691-0.04560.233-21.9366-54.332739.8391
282.81130.30361.17083.10570.63862.6516-0.0579-0.26840.01230.16160.1047-0.07550.0775-0.0668-0.02170.2030.0723-0.03360.2167-0.05980.1671-26.4264-46.436642.7435
292.2659-0.03961.74295.18195.77866.89890.02210.08470.08980.2060.3277-0.45380.32210.2561-0.3930.3048-0.0565-0.07990.2539-0.01250.2217-22.1867-39.33536.5999
303.5719-0.4073-1.27963.51252.73154.1901-0.41210.38010.1749-0.4214-0.1504-0.0594-0.1346-0.4710.57320.3909-0.0361-0.06220.324-0.01810.2053-23.3726-38.726632.8003
311.99241.04431.14893.9191-1.63751.9936-0.02110.00170.43510.04190.67840.0294-0.42120.137-0.68660.20890.0571-0.05330.3236-0.08070.3419-27.2573-39.174338.5263
326.72916.8411-1.76099.9524-2.16630.63080.1317-1.41930.63661.52590.09510.4295-0.14290.0285-0.10140.49370.15160.01270.7313-0.14050.3517-23.0995-39.033459.0539
333.84531.74711.5331.8322.09227.70960.08440.4546-0.2058-0.14640.2895-0.5192-0.15460.6324-0.36930.23130.0284-0.08020.3006-0.0490.2261-15.1052-46.574735.0807
346.50844.75695.57627.0836.3977.5446-0.16810.556-0.3362-0.03450.5936-0.3357-0.16860.7199-0.29830.24280.0237-0.0550.3898-0.10420.3004-16.245-49.914835.9813
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 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 167 )
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 191 )
9X-RAY DIFFRACTION9chain 'A' and (resid 192 through 204 )
10X-RAY DIFFRACTION10chain 'A' and (resid 205 through 220 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 20 )
12X-RAY DIFFRACTION12chain 'B' and (resid 21 through 86 )
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 133 )
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 167 )
15X-RAY DIFFRACTION15chain 'B' and (resid 168 through 179 )
16X-RAY DIFFRACTION16chain 'B' and (resid 180 through 191 )
17X-RAY DIFFRACTION17chain 'B' and (resid 192 through 204 )
18X-RAY DIFFRACTION18chain 'B' and (resid 205 through 220 )
19X-RAY DIFFRACTION19chain 'C' and (resid 3 through 20 )
20X-RAY DIFFRACTION20chain 'C' and (resid 21 through 32 )
21X-RAY DIFFRACTION21chain 'C' and (resid 33 through 86 )
22X-RAY DIFFRACTION22chain 'C' and (resid 87 through 110 )
23X-RAY DIFFRACTION23chain 'C' and (resid 111 through 151 )
24X-RAY DIFFRACTION24chain 'C' and (resid 152 through 167 )
25X-RAY DIFFRACTION25chain 'C' and (resid 168 through 179 )
26X-RAY DIFFRACTION26chain 'C' and (resid 180 through 220 )
27X-RAY DIFFRACTION27chain 'D' and (resid 3 through 68 )
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 133 )
29X-RAY DIFFRACTION29chain 'D' and (resid 134 through 151 )
30X-RAY DIFFRACTION30chain 'D' and (resid 152 through 167 )
31X-RAY DIFFRACTION31chain 'D' and (resid 168 through 179 )
32X-RAY DIFFRACTION32chain 'D' and (resid 180 through 191 )
33X-RAY DIFFRACTION33chain 'D' and (resid 192 through 204 )
34X-RAY DIFFRACTION34chain 'D' and (resid 205 through 220 )

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