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- PDB-3ogo: Structure of the GFP:GFP-nanobody complex at 2.8 A resolution in ... -

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Basic information

Entry
Database: PDB / ID: 3ogo
TitleStructure of the GFP:GFP-nanobody complex at 2.8 A resolution in spacegroup P21212
Components
  • GFP-nanobody
  • Green fluorescent protein
KeywordsFLUORESCENT PROTEIN/IMMUNE SYSTEM / GFP / GFP-nanobody / beta-barrel / antibody / LUMINESCENT PROTEIN-IMMUNE SYSTEM complex / FLUORESCENT PROTEIN-IMMUNE SYSTEM complex
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
ISOPROPYL ALCOHOL / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
CAMELUS DROMEDARIUS (Arabian camel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKubala, M.H. / Kovtun, O. / Alexandrov, K. / Collins, B.M.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.
Authors: Kubala, M.H. / Kovtun, O. / Alexandrov, K. / Collins, B.M.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionAug 25, 2010ID: 3MIQ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
E: GFP-nanobody
F: GFP-nanobody
G: GFP-nanobody
H: GFP-nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,80011
Polymers167,6208
Non-polymers1803
Water5,621312
1
A: Green fluorescent protein
E: GFP-nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9653
Polymers41,9052
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
G: GFP-nanobody


Theoretical massNumber of molelcules
Total (without water)41,9052
Polymers41,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein
H: GFP-nanobody


Theoretical massNumber of molelcules
Total (without water)41,9052
Polymers41,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein
F: GFP-nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0254
Polymers41,9052
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.100, 147.600, 101.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 3:64 or resseq 68:230 )
211chain D and (resseq 3:64 or resseq 68:230 )
112chain A and (resseq 3:64 or resseq 68:228 )
212chain B and (resseq 3:64 or resseq 68:228 )
113chain E and (resseq 3:116 )
213chain F and (resseq 3:116 )
313chain G and (resseq 3:116 )
413chain H and (resseq 3:116 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Green fluorescent protein /


Mass: 28087.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Antibody
GFP-nanobody


Mass: 13817.321 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMELUS DROMEDARIUS (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 4000, 20% isopropanol, 0.1M trisodium citrate dihydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→42.43 Å / Num. all: 52511 / Num. obs: 48206 / % possible obs: 91.8 % / Observed criterion σ(I): 2.9 / Redundancy: 4.5 % / Biso Wilson estimate: 42.27 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.9 / % possible all: 73

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.432 Å / SU ML: 0.34 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 2300 5.03 %5% random
Rwork0.2018 ---
obs0.2043 45703 86.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.186 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.9691 Å20 Å2-0 Å2
2--1.2735 Å20 Å2
3----5.2426 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10879 0 12 312 11203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911139
X-RAY DIFFRACTIONf_angle_d1.17515057
X-RAY DIFFRACTIONf_dihedral_angle_d16.9624122
X-RAY DIFFRACTIONf_chiral_restr0.0771598
X-RAY DIFFRACTIONf_plane_restr0.0051965
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1779X-RAY DIFFRACTIONPOSITIONAL
12D1779X-RAY DIFFRACTIONPOSITIONAL0.046
21A1773X-RAY DIFFRACTIONPOSITIONAL
22B1773X-RAY DIFFRACTIONPOSITIONAL0.055
31E884X-RAY DIFFRACTIONPOSITIONAL
32F884X-RAY DIFFRACTIONPOSITIONAL0.044
33G884X-RAY DIFFRACTIONPOSITIONAL0.044
34H884X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.90050.33681590.26833095X-RAY DIFFRACTION63
2.9005-3.01660.34071950.26943333X-RAY DIFFRACTION68
3.0166-3.15380.32722180.27373713X-RAY DIFFRACTION76
3.1538-3.320.32222360.25344173X-RAY DIFFRACTION85
3.32-3.5280.29462630.22964659X-RAY DIFFRACTION94
3.528-3.80020.27142420.21034800X-RAY DIFFRACTION97
3.8002-4.18230.23842320.18084759X-RAY DIFFRACTION95
4.1823-4.78680.17612480.14234874X-RAY DIFFRACTION97
4.7868-6.02810.18732450.13834940X-RAY DIFFRACTION97
6.0281-42.43710.19612620.18165057X-RAY DIFFRACTION96

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