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- PDB-7cz0: Crystal structure of a thermostable green fluorescent protein (TG... -

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Basic information

Entry
Database: PDB / ID: 7cz0
TitleCrystal structure of a thermostable green fluorescent protein (TGP) with a synthetic nanobody (Sb92)
Components
  • Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
  • Thermostable green fluorescent protein (TGP)
KeywordsFLUORESCENT PROTEIN / complex / GFP / nanobody / single-chain antibody / sybody / synthetic antibody / TGP / thermostable green fluorescent protein
Function / homologyACETATE ION / CACODYLATE ION / CACODYLIC ACID
Function and homology information
Biological speciesGalaxea fascicularis (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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: To Be Published
Title: An improved fluorescent protein tag and its nanobodies for membrane protein expression, stability assay, and purification
Authors: Cai, H. / Yao, H. / Li, T. / Hutter, C. / Tang, Y. / Li, Y. / Seeger, M. / Li, D.
History
DepositionSep 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / 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 / _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 (TGP)
B: Thermostable green fluorescent protein (TGP)
C: Thermostable green fluorescent protein (TGP)
D: Thermostable green fluorescent protein (TGP)
E: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
F: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
G: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
H: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,45223
Polymers170,0458
Non-polymers1,40615
Water0
1
A: Thermostable green fluorescent protein (TGP)
E: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0187
Polymers42,5112
Non-polymers5065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermostable green fluorescent protein (TGP)
F: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0318
Polymers42,5112
Non-polymers5206
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thermostable green fluorescent protein (TGP)
G: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6033
Polymers42,5112
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thermostable green fluorescent protein (TGP)
H: Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7995
Polymers42,5112
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.245, 130.154, 171.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Antibody , 2 types, 8 molecules ABCDEFGH

#1: Protein
Thermostable green fluorescent protein (TGP)


Mass: 26699.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Uniprot A8CLT2 / Source: (gene. exp.) Galaxea fascicularis (invertebrata) / Plasmid: pEC / Details (production host): pET-based vector / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Antibody
Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)


Mass: 15811.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pEC / Details (production host): pET-based vector / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 15 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2

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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: 3.12 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.4 %(w/v) PEG 8000, 160mM calcium acetate, 20% (v/v) glycerol, 80mM sodium cacodylate / HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.77→47.62 Å / Num. obs: 54942 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 56.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.062 / Net I/σ(I): 9.2
Reflection shellResolution: 2.77→2.85 Å / Redundancy: 7 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4418 / CC1/2: 0.78 / Rpim(I) all: 0.651 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZ2

6lz2


Resolution: 2.77→47.62 Å / SU ML: 0.3827 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3841
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 2720 4.96 %
Rwork0.2023 52071 -
obs0.2042 54791 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.23 Å2
Refinement stepCycle: LAST / Resolution: 2.77→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10522 0 84 0 10606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003810864
X-RAY DIFFRACTIONf_angle_d0.715514674
X-RAY DIFFRACTIONf_chiral_restr0.04871516
X-RAY DIFFRACTIONf_plane_restr0.00341899
X-RAY DIFFRACTIONf_dihedral_angle_d21.76031542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.820.42271310.33842702X-RAY DIFFRACTION99.79
2.82-2.870.43711290.332725X-RAY DIFFRACTION99.72
2.87-2.930.3591430.30412696X-RAY DIFFRACTION99.75
2.93-30.31681390.28632708X-RAY DIFFRACTION99.68
3-3.070.28651510.26342678X-RAY DIFFRACTION99.68
3.07-3.140.31851530.2572701X-RAY DIFFRACTION99.72
3.14-3.230.29251410.24042724X-RAY DIFFRACTION99.76
3.23-3.320.24641310.22212718X-RAY DIFFRACTION99.86
3.32-3.430.27751450.22352732X-RAY DIFFRACTION99.79
3.43-3.550.27531350.21982728X-RAY DIFFRACTION99.86
3.55-3.70.25281440.2062717X-RAY DIFFRACTION99.9
3.7-3.860.25611300.19572748X-RAY DIFFRACTION99.86
3.86-4.070.21791740.182732X-RAY DIFFRACTION99.97
4.07-4.320.22481360.16912741X-RAY DIFFRACTION99.79
4.32-4.660.17951510.15492740X-RAY DIFFRACTION99.93
4.66-5.120.18021550.15012763X-RAY DIFFRACTION99.9
5.12-5.860.21671380.16332785X-RAY DIFFRACTION99.9
5.86-7.380.20291490.19862824X-RAY DIFFRACTION99.9
7.38-47.620.19761450.19282909X-RAY DIFFRACTION98.01

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