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- PDB-6lz2: Crystal structure of a thermostable green fluorescent protein (TG... -

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Basic information

Entry
Database: PDB / ID: 6lz2
TitleCrystal structure of a thermostable green fluorescent protein (TGP) with a synthetic nanobody (Sb44)
Components
  • Thermostable green fluorescent protein
  • synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
KeywordsFLUORESCENT PROTEIN / complex / GFP / nanobody / single-chain antibody / sybody / synthetic antibody / TGP / thermostable green fluorescent protein
Function / homologyACETATE ION
Function and homology information
Biological speciesGalaxea fascicularis (invertebrata)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsCai, H. / Yao, H. / Li, T. / Hutter, C. / Tang, Y. / Li, Y. / Seeger, M. / Li, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31870726 China
CitationJournal: Commun Biol / Year: 2020
Title: An improved fluorescent tag and its nanobodies for membrane protein expression, stability assay, and purification.
Authors: Cai, H. / Yao, H. / Li, T. / Hutter, C.A.J. / Li, Y. / Tang, Y. / Seeger, M.A. / Li, D.
History
DepositionFeb 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable green fluorescent protein
B: synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
C: Thermostable green fluorescent protein
D: synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,12313
Polymers84,5344
Non-polymers5889
Water8,449469
1
A: Thermostable green fluorescent protein
B: synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3725
Polymers42,2672
Non-polymers1053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-35 kcal/mol
Surface area14670 Å2
MethodPISA
2
C: Thermostable green fluorescent protein
D: synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7518
Polymers42,2672
Non-polymers4836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-11 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.610, 83.486, 184.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

#1: Protein Thermostable green fluorescent protein


Mass: 26699.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: uniprot A8CLT2 / Source: (gene. exp.) Galaxea fascicularis (invertebrata) / Gene: Green fluorescent GFP-like protein / Plasmid: pEC / Details (production host): pET based vector / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Antibody synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)


Mass: 15567.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pEC / Details (production host): pET based vector / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 478 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 % / Description: 0.2-mm plate clusters
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium acetate, 25 %(w/v) polyethylene glycol 3350, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→49.53 Å / Num. obs: 52046 / % possible obs: 99.3 % / Redundancy: 13.1 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.037 / Χ2: 0.94 / Net I/σ(I): 13.9
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.694 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3497 / CC1/2: 0.67 / CC star: 0.896 / Rpim(I) all: 0.504 / Χ2: 0.84 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tza, 5m13

4tza

5m13


Resolution: 2.03→45.04 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3682
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1990 3.84 %Random selection
Rwork0.1747 ---
obs0.1763 51766 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.4 Å2
Refinement stepCycle: LAST / Resolution: 2.03→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 38 469 5815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745663
X-RAY DIFFRACTIONf_angle_d0.92997672
X-RAY DIFFRACTIONf_chiral_restr0.0573785
X-RAY DIFFRACTIONf_plane_restr0.00541002
X-RAY DIFFRACTIONf_dihedral_angle_d16.9526824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.31471270.27263216X-RAY DIFFRACTION90.89
2.09-2.140.29321410.23123520X-RAY DIFFRACTION99.97
2.14-2.210.2811400.21373505X-RAY DIFFRACTION99.89
2.21-2.280.26931420.20923541X-RAY DIFFRACTION99.95
2.28-2.360.23421410.19633520X-RAY DIFFRACTION99.86
2.36-2.450.23331430.19873570X-RAY DIFFRACTION99.97
2.45-2.560.28271420.20713532X-RAY DIFFRACTION99.95
2.56-2.70.26511410.19253537X-RAY DIFFRACTION99.95
2.7-2.870.251430.19813589X-RAY DIFFRACTION99.95
2.87-3.090.26381430.19863568X-RAY DIFFRACTION100
3.09-3.40.19191430.17553578X-RAY DIFFRACTION100
3.4-3.890.2011450.15653619X-RAY DIFFRACTION100
3.89-4.90.17931470.12973674X-RAY DIFFRACTION100
4.9-45.040.16311520.16083807X-RAY DIFFRACTION99.45

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