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- PDB-3ed8: Application of the superfolder YFP bimolecular fluorescence compl... -

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Basic information

Entry
Database: PDB / ID: 3ed8
TitleApplication of the superfolder YFP bimolecular fluorescence complementation for studying protein-protein interactions in vitro
Componentsyellow fluorescence protein
KeywordsLUMINESCENT PROTEIN / superfolder / bimolecular fluorescence complementation
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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOttmann, C. / Weyand, M.
CitationJournal: Biol.Chem. / Year: 2009
Title: Applicability of superfolder YFP bimolecular fluorescence complementation in vitro.
Authors: Ottmann, C. / Weyand, M. / Wolf, A. / Kuhlmann, J. / Ottmann, C.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 21, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: yellow fluorescence protein
B: yellow fluorescence protein
C: yellow fluorescence protein
D: yellow fluorescence protein
E: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)146,6965
Polymers146,6965
Non-polymers00
Water3,387188
1
A: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: yellow fluorescence protein


Theoretical massNumber of molelcules
Total (without water)29,3391
Polymers29,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.040, 123.040, 247.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
yellow fluorescence protein


Mass: 29339.270 Da / Num. of mol.: 5
Mutation: S30R,Y39I,F64L,F99S,N105K,E111V,I128T,Y145F,M153T,V163A,K166T,I167V,I171V,S205T,A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLY65,TYR66,GLY67 CIRCULARIZED INTO ONE CHROMOPHORE, CRO

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl pH 8.5, 20 % ethanol, 12 % TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9781 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Aug 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.7→45.98 Å / Num. all: 52991 / Num. obs: 52991 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 61.544 Å2 / Rsym value: 0.111 / Net I/σ(I): 16.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 4.16 / Num. unique all: 5389 / Rsym value: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0054refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.084 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21774 2650 5 %RANDOM
Rwork0.17434 ---
obs0.17656 50339 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.262 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8815 0 0 188 9003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.95912332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.76951136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.924.834422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.458151413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0821534
X-RAY DIFFRACTIONr_chiral_restr0.1050.21377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216981
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5261.55635
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02829063
X-RAY DIFFRACTIONr_scbond_it1.79733445
X-RAY DIFFRACTIONr_scangle_it3.014.53260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 192 -
Rwork0.254 3636 -
obs--100 %
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)
13.7826-0.1948-0.26573.1952-0.38161.7937-0.10120.2795-0.0345-0.24280.0764-0.1582-0.0487-0.00310.02480.25950.02190.02840.0299-0.00210.1031-21.320327.6594-25.7692
21.97510.25560.03832.76090.75962.5794-0.2530.07080.3028-0.2263-0.07930.8325-0.0032-0.08340.33240.2109-0.0285-0.13920.012-0.00160.3499-24.9812-2.9256-37.94
34.00340.65380.30423.93721.22552.6931-0.44220.297-0.3124-0.05910.3762-0.10350.1040.89560.0660.2683-0.05370.01740.39980.04940.04911.8853-13.2098-46.0529
42.2575-0.57450.05072.64170.17722.1316-0.2168-0.53770.07980.51190.1551-0.1779-0.202-0.06410.06170.30250.0878-0.08790.16040.02420.1317-13.790420.91152.415
54.61360.26760.36373.2343-0.04042.4240.04660.35010.2478-1.0026-0.1297-0.8381-0.2620.67330.08310.697-0.10270.21590.60960.21730.890533.826217.324-8.7893
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 254
2X-RAY DIFFRACTION2B2 - 255
3X-RAY DIFFRACTION3C2 - 255
4X-RAY DIFFRACTION4D2 - 255
5X-RAY DIFFRACTION5E3 - 255

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