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- PDB-6ir7: Green fluorescent protein variant GFPuv with the modification to ... -

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Basic information

Entry
Database: PDB / ID: 6ir7
TitleGreen fluorescent protein variant GFPuv with the modification to 6-hydroxynorleucine at the C-terminus
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN
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
6-HYDROXY-L-NORLEUCINE / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.277 Å
AuthorsNakatani, T. / Yasui, N. / Yamashita, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03644 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)25891017 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Specific modification at the C-terminal lysine residue of the green fluorescent protein variant, GFPuv, expressed in Escherichia coli.
Authors: Nakatani, T. / Yasui, N. / Tamura, I. / Yamashita, A.
History
DepositionNov 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1204
Polymers26,6821
Non-polymers4383
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.295, 51.152, 48.506
Angle α, β, γ (deg.)90.00, 100.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein


Mass: 26681.920 Da / Num. of mol.: 1 / Mutation: Q80R, F99S, M153T, V163A, A206K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P42212
#2: Chemical ChemComp-LDO / 6-HYDROXY-L-NORLEUCINE


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE THR 65 HAS BEEN MUTATED TO SER 65. RESIDUES SER 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 65 HAS BEEN MUTATED TO SER 65. RESIDUES SER 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CRO 66

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate, 0.1 M MES pH 6.5, 30% PEGMME5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 56911 / % possible obs: 96.3 % / Redundancy: 3.1 % / Rsym value: 0.071 / Net I/σ(I): 27.8
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 7.2 / Num. unique obs: 2566 / Rsym value: 0.248 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9C

1b9c


Resolution: 1.277→47.649 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 2889 5.08 %Random selection
Rwork0.1748 ---
obs0.1758 56891 96.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.277→47.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 17 368 2249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061978
X-RAY DIFFRACTIONf_angle_d1.142687
X-RAY DIFFRACTIONf_dihedral_angle_d16.357744
X-RAY DIFFRACTIONf_chiral_restr0.047289
X-RAY DIFFRACTIONf_plane_restr0.006347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2767-1.29770.2121970.19732314X-RAY DIFFRACTION87
1.2977-1.320.20051350.19472540X-RAY DIFFRACTION96
1.32-1.3440.19621260.18122591X-RAY DIFFRACTION96
1.344-1.36990.19431350.18182539X-RAY DIFFRACTION97
1.3699-1.39790.17191360.18362563X-RAY DIFFRACTION96
1.3979-1.42830.19581370.1792498X-RAY DIFFRACTION94
1.4283-1.46150.191260.17422576X-RAY DIFFRACTION97
1.4615-1.4980.19571260.17252603X-RAY DIFFRACTION98
1.498-1.53850.18951420.16622567X-RAY DIFFRACTION97
1.5385-1.58380.19661510.15952554X-RAY DIFFRACTION96
1.5838-1.63490.18441460.15172567X-RAY DIFFRACTION96
1.6349-1.69340.16751370.16152549X-RAY DIFFRACTION96
1.6934-1.76120.18031630.1622590X-RAY DIFFRACTION98
1.7612-1.84130.18361460.16352599X-RAY DIFFRACTION98
1.8413-1.93840.17851330.16392652X-RAY DIFFRACTION99
1.9384-2.05990.18921610.15652607X-RAY DIFFRACTION98
2.0599-2.21890.18341400.15952613X-RAY DIFFRACTION98
2.2189-2.44220.19791220.17162679X-RAY DIFFRACTION99
2.4422-2.79560.1961600.182603X-RAY DIFFRACTION98
2.7956-3.52190.18131240.1852563X-RAY DIFFRACTION95
3.5219-47.68190.22651460.19122635X-RAY DIFFRACTION95
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)
13.4373-0.43051.36351.072-0.3451.40190.0909-0.0242-0.1587-0.14890.03270.01880.0927-0.0993-0.11270.09840.00140.00820.0784-0.02210.09184.9092-5.477-0.0566
20.84780.1346-0.07950.691-0.13140.9118-0.0014-0.013-0.0094-0.02240.0063-0.00780.0355-0.0197-0.0140.09180.00520.00010.08-0.01130.09188.5271-1.01665.6415
31.3793-0.14220.53340.4724-0.16251.0713-0.00420.0664-0.0821-0.04050.0083-0.05550.02380.0425-0.01110.0965-0.00290.00370.0797-0.0050.090215.0878-5.408-0.2713
41.2947-0.4433-0.53321.00590.37521.2031-0.167-0.26740.04830.1870.1557-0.1476-0.00710.10720.02270.1197-0.0017-0.01170.1369-0.01850.109321.21631.465718.321
50.9480.16450.18930.8272-0.30090.8750.01530.02830.0132-0.07630.0029-0.0979-0.02250.0584-0.02980.1025-0.00630.01560.0967-0.0030.119419.41044.2487-1.6791
60.4874-0.29690.23170.3532-0.03070.12620.01680.02280.06340.04690.01790.0278-0.0852-0.0383-0.03980.1097-0.00620.00830.1024-0.00450.09996.38188.99654.2815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 198 )
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 237 )

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