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- PDB-3g9a: Green fluorescent protein bound to minimizer nanobody -

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Basic information

Entry
Database: PDB / ID: 3g9a
TitleGreen fluorescent protein bound to minimizer nanobody
Components
  • Green fluorescent protein
  • Minimizer
KeywordsFLUORESCENT PROTEIN/IMMUNE SYSTEM / Antibody Complex / Chromophore / Luminescence / Photoprotein / FLUORESCENT PROTEIN-IMMUNE SYSTEM COMPLEX / NANOBODY
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 / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.614 Å
AuthorsKirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Delucci, C.C. / Cardoso, M.C. ...Kirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Delucci, C.C. / Cardoso, M.C. / Leonhardt, H. / Hopfner, K.-P. / Rothbauer, U.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Modulation of protein properties in living cells using nanobodies
Authors: Kirchhofer, A. / Helma, J. / Schmidthals, K. / Frauer, C. / Cui, S. / Karcher, A. / Pellis, M. / Muyldermans, S. / Deulcci, C.C. / Cardoso, M.C. / Leonhardt, H. / Hopfner, K.-P. / Rothbauer, U.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Database references / Source and taxonomy
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
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 / 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
B: Minimizer


Theoretical massNumber of molelcules
Total (without water)41,7832
Polymers41,7832
Non-polymers00
Water12,340685
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.780, 81.620, 94.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein /


Mass: 26783.088 Da / Num. of mol.: 1 / Mutation: S2G, Q80R, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pRSet5D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P42212
#2: Antibody Minimizer


Mass: 14999.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE CHAIN A, THE SKIPPED RESIDUE NUMBERS 65, 67 ARE DUE TO THE CHROMOPHORE. IN THE CHAIN B, ...IN THE CHAIN A, THE SKIPPED RESIDUE NUMBERS 65, 67 ARE DUE TO THE CHROMOPHORE. IN THE CHAIN B, THERE ARE MANY RESIDUES WITH INSERTION CODES

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Mes pH 6.5, 30% PEG 8000, 15% Glycerol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98137 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2008
RadiationMonochromator: 0.98137 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98137 Å / Relative weight: 1
ReflectionResolution: 1.61→47 Å / Num. all: 51266 / Num. obs: 49989 / % possible obs: 97.5 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 3.85 % / Rsym value: 0.057 / Net I/σ(I): 16.91
Reflection shellResolution: 1.61→1.71 Å / Mean I/σ(I) obs: 2.84 / Rsym value: 0.391 / % possible all: 86.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.614→47 Å / SU ML: 1.31 / σ(F): 1.97 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2542 5.09 %random
Rwork0.1606 ---
all0.168 49991 --
obs0.1623 49988 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.698 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0234 Å20 Å20 Å2
2---3.6737 Å20 Å2
3---5.2755 Å2
Refinement stepCycle: LAST / Resolution: 1.614→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 685 3457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052887
X-RAY DIFFRACTIONf_angle_d1.043910
X-RAY DIFFRACTIONf_dihedral_angle_d15.6981060
X-RAY DIFFRACTIONf_chiral_restr0.073426
X-RAY DIFFRACTIONf_plane_restr0.007510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.614-1.6450.24331080.2355180067
1.645-1.67860.26871610.2099245694
1.6786-1.71510.24131470.1993265099
1.7151-1.7550.23551260.1846264599
1.755-1.79890.20361480.17072643100
1.7989-1.84750.18031450.156267299
1.8475-1.90190.18611430.1528264099
1.9019-1.96330.17011540.15112673100
1.9633-2.03340.17471480.14512666100
2.0334-2.11490.18661420.1442672100
2.1149-2.21110.18721410.15232699100
2.2111-2.32770.20691300.15662691100
2.3277-2.47350.20561320.16022701100
2.4735-2.66450.20781360.16522720100
2.6645-2.93260.19921300.16622720100
2.9326-3.35680.18251460.14982746100
3.3568-4.22880.15121450.13182767100
4.2288-47.26020.1671600.15742885100

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