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- PDB-6xzf: Nanobody in complex with eGFP -

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Basic information

Entry
Database: PDB / ID: 6xzf
TitleNanobody in complex with eGFP
Components
  • Nanobody targeted against eGFP
  • eGFP
KeywordsIMMUNE SYSTEM / Nanobody
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / TERBIUM(III) ION / Green fluorescent protein
Function and homology information
Biological speciesLama glama (llama)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T.
CitationJournal: To Be Published
Title: Engineered nanobodies with a lanthanide binding motif for crystallographic phasing
Authors: Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T.
History
DepositionFeb 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
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 / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Oct 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

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Assembly

Deposited unit
A: eGFP
B: Nanobody targeted against eGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8463
Polymers41,6872
Non-polymers1591
Water3,963220
1
A: eGFP


Theoretical massNumber of molelcules
Total (without water)26,8251
Polymers26,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody targeted against eGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0212
Polymers14,8621
Non-polymers1591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.335, 69.335, 169.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein eGFP


Mass: 26825.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aequorea victoria (jellyfish) / References: UniProt: P42212*PLUS
#2: Antibody Nanobody targeted against eGFP


Mass: 14862.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaAcetate pH 4.6 8 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.69→48.95 Å / Num. obs: 52868 / % possible obs: 98.3 % / Redundancy: 18.7 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.016 / Rrim(I) all: 0.068 / Net I/σ(I): 22.4 / Num. measured all: 989184 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.727.72.141413418310.1130.7812.2950.968.7
9.09-48.9515.50.03766244270.9990.0090.03869.899.4

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.95 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 2110 4.74 %
Rwork0.1732 42449 -
obs0.1746 44559 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 1 220 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152900
X-RAY DIFFRACTIONf_angle_d1.28093929
X-RAY DIFFRACTIONf_chiral_restr0.0709415
X-RAY DIFFRACTIONf_plane_restr0.0088518
X-RAY DIFFRACTIONf_dihedral_angle_d18.99461071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.27831250.25812801X-RAY DIFFRACTION99.8
1.84-1.890.27031270.23882806X-RAY DIFFRACTION99.86
1.89-1.940.27621450.2282775X-RAY DIFFRACTION99.9
1.94-20.22771350.20672783X-RAY DIFFRACTION99.9
2-2.060.2091350.19662786X-RAY DIFFRACTION99.9
2.06-2.130.23871380.19472792X-RAY DIFFRACTION99.97
2.13-2.220.23671760.17652768X-RAY DIFFRACTION99.93
2.22-2.320.22781410.18282819X-RAY DIFFRACTION100
2.32-2.440.20881450.16852799X-RAY DIFFRACTION99.97
2.44-2.60.19881370.16662821X-RAY DIFFRACTION100
2.6-2.80.21751180.17172861X-RAY DIFFRACTION100
2.8-3.080.21311470.17812830X-RAY DIFFRACTION100
3.08-3.520.22281460.17742870X-RAY DIFFRACTION100
3.52-4.440.19831290.14922905X-RAY DIFFRACTION99.97
4.44-48.950.16261660.16553033X-RAY DIFFRACTION99.88

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