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- PDB-4xgy: GFP based antibody (fluorobody) -

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Basic information

Entry
Database: PDB / ID: 4xgy
TitleGFP based antibody (fluorobody)
ComponentsGreen fluorescent protein, mAb LCDR3, Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / Fluorobody / GFP / CDR3
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 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Vibrio parahaemolyticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsShi, N. / Chen, Y.G. / Wang, S.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: The structure of a GFP-based antibody (fluorobody) to TLH, a toxin from Vibrio parahaemolyticus.
Authors: Chen, Y. / Huang, X. / Wang, R. / Wang, S. / Shi, N.
History
DepositionJan 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein, mAb LCDR3, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6153
Polymers33,8181
Non-polymers7972
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-1 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 63.350, 125.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21A-508-

HOH

31A-622-

HOH

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Components

#1: Protein Green fluorescent protein, mAb LCDR3, Green fluorescent protein


Mass: 33817.828 Da / Num. of mol.: 1
Mutation: R30S,N39Y,L64F,R80Q,S99F,T105N,F145Y,T153M,A163V,V219A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of residues 2-173 from Green fluorescent protein, mAb LCDR3, residues 174-238 from Green fluorescent protein, and C-terminal expression tag
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Vibrio parahaemolyticus (bacteria), (gene. exp.) synthetic construct (others)
Gene: GFP / Plasmid: pGEPi / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212, UniProt: A0A059PIQ0*PLUS
#2: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 40% PEG400, 0.1M Hepes, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.494→31.68 Å / Num. obs: 42096 / % possible obs: 99.33 % / Redundancy: 23.3 % / Net I/σ(I): 264.06

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
iMOSFLMdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b3p

2b3p


Resolution: 1.494→31.675 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1665 1996 4.74 %Random selectio
Rwork0.1451 ---
obs0.1461 42094 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.494→31.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 32 303 2239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092069
X-RAY DIFFRACTIONf_angle_d1.3352797
X-RAY DIFFRACTIONf_dihedral_angle_d14.758778
X-RAY DIFFRACTIONf_chiral_restr0.072299
X-RAY DIFFRACTIONf_plane_restr0.006367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.494-1.53140.21161610.16742797X-RAY DIFFRACTION100
1.5314-1.57280.19461510.15992819X-RAY DIFFRACTION100
1.5728-1.61910.18341300.15882846X-RAY DIFFRACTION100
1.6191-1.67130.19171250.15492846X-RAY DIFFRACTION100
1.6713-1.7310.18331260.14742853X-RAY DIFFRACTION100
1.731-1.80030.171400.15172852X-RAY DIFFRACTION100
1.8003-1.88230.17181410.14732857X-RAY DIFFRACTION100
1.8823-1.98150.16211490.1422864X-RAY DIFFRACTION100
1.9815-2.10560.15391470.142852X-RAY DIFFRACTION100
2.1056-2.26820.16931580.13512869X-RAY DIFFRACTION100
2.2682-2.49630.18071730.13662858X-RAY DIFFRACTION100
2.4963-2.85730.15391220.14212942X-RAY DIFFRACTION100
2.8573-3.59910.15191380.13782953X-RAY DIFFRACTION100
3.5991-31.6820.16111350.15332890X-RAY DIFFRACTION92
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)
11.17250.2703-0.04281.5393-0.10592.00280.0708-0.06180.00560.0304-0.09780.0980.171-0.03680.00580.0864-0.00290.01420.0627-0.01440.1096-10.180510.1732-5.1016
23.2427-1.5126-0.03675.8268-6.02557.16750.1002-0.5195-0.23590.1309-0.0133-0.0038-0.09020.2837-0.07750.2232-0.0714-0.0020.20350.01930.206-10.4222-9.941210.4412
30.9485-0.37350.11551.0427-0.38412.12740.06360.01940.0339-0.1134-0.0824-0.02870.22740.1483-0.01010.10310.00940.01560.0624-0.00450.108-5.29078.7662-8.2929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 177 )
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 243 )

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