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- PDB-6un6: Crystal structure of green fluorescent protein (GFP); S65T, Y66(3... -

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Basic information

Entry
Database: PDB / ID: 6un6
TitleCrystal structure of green fluorescent protein (GFP); S65T, Y66(3-NO2Y); ih circular permutant (50-51)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, C.-Y. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems.
Authors: Lin, C.Y. / Boxer, S.G.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)56,5192
Polymers56,5192
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area19250 Å2
Unit cell
Length a, b, c (Å)47.947, 67.719, 58.363
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein /


Mass: 28259.525 Da / Num. of mol.: 2
Mutation: A72S, Q80R, T105K, E111V, I128T, K166T, I167V, S205T, A206V, S232R, Y241I, C250S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp, GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: A0A059PIQ0, UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 34% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→38.528 Å / Num. obs: 57467 / % possible obs: 98.1 % / Redundancy: 13.26 % / Biso Wilson estimate: 21.78 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 12.56 % / Rmerge(I) obs: 2.238 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 4040 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.13RC2_2986refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OFK

6ofk


Resolution: 1.5→38.53 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.16
RfactorNum. reflection% reflection
Rfree0.181 2862 5 %
Rwork0.159 --
obs0.161 57231 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 0 263 3885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5260.2921270.27132417X-RAY DIFFRACTION88
1.526-1.55370.22951440.24442724X-RAY DIFFRACTION98
1.5537-1.58360.28041430.22722723X-RAY DIFFRACTION99
1.5836-1.61590.22521440.21612738X-RAY DIFFRACTION98
1.6159-1.6510.2321440.21062737X-RAY DIFFRACTION99
1.651-1.68950.26841430.19852723X-RAY DIFFRACTION99
1.6895-1.73170.21511440.18672733X-RAY DIFFRACTION99
1.7317-1.77850.20961440.17922730X-RAY DIFFRACTION99
1.7785-1.83090.19751410.18082679X-RAY DIFFRACTION98
1.8309-1.890.20481400.17452657X-RAY DIFFRACTION96
1.89-1.95750.19851440.16682736X-RAY DIFFRACTION99
1.9575-2.03590.19151450.16162754X-RAY DIFFRACTION99
2.0359-2.12850.15191440.15192752X-RAY DIFFRACTION99
2.1285-2.24070.18161460.15442758X-RAY DIFFRACTION99
2.2407-2.38110.17891450.15672759X-RAY DIFFRACTION100
2.3811-2.56490.19371430.1662722X-RAY DIFFRACTION98
2.5649-2.8230.20511430.17112713X-RAY DIFFRACTION97
2.823-3.23130.16971460.15772760X-RAY DIFFRACTION99
3.2313-4.07030.1761460.13832768X-RAY DIFFRACTION99
4.0703-38.5280.13951460.13992786X-RAY DIFFRACTION98
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)
11.39030.31550.27151.61680.34121.33970.08-0.14920.04550.0167-0.10650.12790.022-0.10920.01980.1593-0.00220.00630.158-0.01630.14373.08558.47120.0954
22.64641.8302-0.86693.2315-0.78352.6382-0.11320.0416-0.2214-0.3088-0.0142-0.20980.3195-0.04260.05250.18540.00510.00960.1477-0.00780.16817.71961.4536-5.5549
31.04850.67240.05832.06590.42071.5680.0774-0.06090.06430.0159-0.1088-0.0219-0.02570.01060.03350.17790.0016-0.00220.1746-0.01370.15457.052913.14091.2632
40.1971-0.43030.28175.12080.19970.62930.5049-0.69990.35140.7765-0.53011.0347-0.0543-0.47390.47570.3423-0.1090.17050.347-0.11620.3782-9.25850.81438.0092
52.46981.1749-1.46232.7241-1.15783.4930.03770.014-0.25940.0422-0.074-0.36270.22440.08570.08340.18980.0038-0.02750.1640.01630.202614.41370.7304-1.1513
67.8213-1.3667-1.74792.90930.13733.14240.1033-0.4361-0.15340.3999-0.1133-0.250.28840.2102-0.00420.2614-0.0556-0.05580.20420.03140.219511.45362.05827.7511
71.9337-0.26270.34642.2763-0.68661.6716-0.1558-0.00410.04650.25390.0626-0.2247-0.15330.1064-0.00680.2055-0.0264-0.01940.1385-0.00250.140115.454421.901430.7268
81.65550.28080.84312.58970.47183.14080.08860.13320.24060.00940.00860.3111-0.1868-0.42940.12540.2224-0.01280.00950.21890.06040.2503-0.302526.455421.229
93.43890.13151.72121.52680.06722.5889-0.07830.01730.27510.1135-0.0143-0.3044-0.29380.17210.06210.2583-0.0532-0.03680.18740.03230.262416.167529.733422.9092
100.79060.2098-0.74171.16630.0771.2961-0.4029-0.02740.53940.33430.0164-0.5211-0.4540.4772-0.10370.2904-0.0587-0.09930.24080.02090.326421.658328.087829.7758
111.5795-0.36670.37831.73490.51821.9702-0.10620.1727-0.1675-0.10460.1010.0630.1416-0.02310.03430.2102-0.0421-0.01710.16740.00880.14739.577213.590721.8296
124.9881-0.7254-4.1911.56761.06813.6714-0.11950.38140.30540.3685-0.0903-0.95220.17670.7429-0.17690.3748-0.146-0.03520.72070.07630.682936.937618.171122.3261
132.1758-0.2215-0.58792.9309-0.17641.4321-0.1767-0.1444-0.19770.33010.1253-0.025-0.0630.00860.02370.24880.0018-0.00410.17540.01640.137311.725614.792533.7717
146.30630.6069-1.64241.8739-0.28533.1164-0.08510.09960.01750.10060.13740.0920.1529-0.1307-0.00630.21760.00030.01440.14680.01640.19689.877410.90828.1363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 54 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 55 THROUGH 78 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 79 THROUGH 177 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 178 THROUGH 204 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 205 THROUGH 229 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 230 THROUGH 243 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 2 THROUGH 78 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 79 THROUGH 98 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 99 THROUGH 125 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 126 THROUGH 148 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 149 THROUGH 177 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 178 THROUGH 196 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 197 THROUGH 229 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 230 THROUGH 243 )

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