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- PDB-8c1x: sfGFP C148 F206 mutant -

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Basic information

Entry
Database: PDB / ID: 8c1x
TitlesfGFP C148 F206 mutant
ComponentsGreen fluorescent protein
KeywordsSIGNALING PROTEIN / GFP / Signalling protein / Fluorescent protein / mutant / enhanced fluorescence / protein engineering
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
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAhmed, R.D. / Rizkallah, P.J. / Jones, D.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To Be Published
Title: sfGFP C148 F206 mutant
Authors: Ahmed, R.D. / Rizkallah, P.J. / Jones, D.D.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Green fluorescent protein
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)104,9314
Polymers104,9314
Non-polymers00
Water4,486249
1
A: Green fluorescent protein

A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,4652
Polymers52,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area20320 Å2
MethodPISA
2
B: Green fluorescent protein

B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,4652
Polymers52,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area20100 Å2
MethodPISA
3
C: Green fluorescent protein

D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,4652
Polymers52,4652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1800 Å2
ΔGint-12 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.489, 73.763, 127.277
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Green fluorescent protein


Mass: 26232.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane, pH 7.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.81532 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81532 Å / Relative weight: 1
ReflectionResolution: 1.89→39.25 Å / Num. obs: 100181 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 10.4
Reflection shellResolution: 1.89→1.93 Å / Num. unique obs: 4910 / CC1/2: 0.225

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.89→39.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 15.284 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24703 4775 4.8 %RANDOM
Rwork0.2065 ---
obs0.20843 95406 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.958 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å2-0.71 Å2
2--1.81 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.89→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 0 249 7591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137609
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177072
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.65310281
X-RAY DIFFRACTIONr_angle_other_deg1.2881.59316356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4485930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03223.269416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.641151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0051534
X-RAY DIFFRACTIONr_chiral_restr0.0770.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021714
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it23.3283711
X-RAY DIFFRACTIONr_mcbond_other23.3273710
X-RAY DIFFRACTIONr_mcangle_it3.0494.9824644
X-RAY DIFFRACTIONr_mcangle_other3.0494.9834645
X-RAY DIFFRACTIONr_scbond_it2.6173.613898
X-RAY DIFFRACTIONr_scbond_other2.6163.613899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1475.2935638
X-RAY DIFFRACTIONr_long_range_B_refined6.71138.0147741
X-RAY DIFFRACTIONr_long_range_B_other6.71237.8747710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.938 Å
RfactorNum. reflection% reflection
Rfree0.448 349 -
Rwork0.453 6900 -
obs--98.37 %
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)
12.43730.20690.09251.42550.00342.4018-0.0220.1444-0.3566-0.10070.0585-0.02510.1877-0.0375-0.03640.0226-0.00740.01250.1208-0.03730.238526.1832-0.176549.4528
22.7087-0.44120.15541.52690.04142.6117-0.0951-0.17860.37710.10980.0867-0.0576-0.2238-0.05160.00840.04660.01630.04390.1232-0.04130.230126.23530.861814.1628
31.5430.2994-0.52192.192-0.58612.19830.0125-0.05580.05040.1242-0.0614-0.1088-0.00180.08450.04890.01950.01770.02530.2292-0.01930.1183-7.1882-20.956229.1864
41.7985-0.3570.73012.3174-0.79492.23470.03080.0855-0.0952-0.152-0.0551-0.1009-0.00130.10490.02430.024-0.01210.04160.2172-0.03040.1209-7.270321.637234.4143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 233
2X-RAY DIFFRACTION2B1 - 233
3X-RAY DIFFRACTION3C3 - 233
4X-RAY DIFFRACTION4D3 - 233

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