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- PDB-8bxp: SfGFP C148 F206 mutant -

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Basic information

Entry
Database: PDB / ID: 8bxp
TitleSfGFP C148 F206 mutant
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / GFP / green fluorescent protein / protein engineering / mutant
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: 1.79 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 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,5232
Polymers52,5232
Non-polymers00
Water4,954275
1
A: Green fluorescent protein

A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,5232
Polymers52,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1820 Å2
ΔGint-12 kcal/mol
Surface area20340 Å2
MethodPISA
2
B: Green fluorescent protein

B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,5232
Polymers52,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.804, 75.016, 125.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Green fluorescent protein


Mass: 26261.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate, 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: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81532 Å / Relative weight: 1
ReflectionResolution: 1.79→50.36 Å / Num. obs: 61413 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 10.5
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 2999 / CC1/2: 0.351

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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: 1.79→50.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.876 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23442 3051 5 %RANDOM
Rwork0.20009 ---
obs0.2018 58326 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--1.74 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.79→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 0 275 3954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173609
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6535287
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5938355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8125485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96923.271214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5315674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9691518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
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_it1.7982.7031910
X-RAY DIFFRACTIONr_mcbond_other1.7982.7021909
X-RAY DIFFRACTIONr_mcangle_it2.7054.0382405
X-RAY DIFFRACTIONr_mcangle_other2.7044.0412406
X-RAY DIFFRACTIONr_scbond_it2.4292.9351991
X-RAY DIFFRACTIONr_scbond_other2.4282.9361992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8334.2982883
X-RAY DIFFRACTIONr_long_range_B_refined6.82331.4354005
X-RAY DIFFRACTIONr_long_range_B_other6.81431.0953964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A16020.08
12B16020.08
21A51280.1
22B51280.1
LS refinement shellResolution: 1.79→1.833 Å
RfactorNum. reflection% reflection
Rfree0.424 213 -
Rwork0.429 4151 -
obs--97.13 %
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)
12.47720.24660.12021.51440.01372.30010.00340.05890.1591-0.09130.0285-0.0493-0.14380.0307-0.03190.01790.00650.02170.08390.00330.11917.34570.115317.2843
21.5549-0.2333-0.57092.08960.46272.0132-0.00320.07340.0646-0.08610.01720.07990.0613-0.0354-0.0140.0084-0.0151-0.00590.1615-0.05060.147741.0016-21.7942.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 233
2X-RAY DIFFRACTION2B2 - 233

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