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- PDB-4xvp: X-ray structure of bGFP-C / EGFP complex -

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Basic information

Entry
Database: PDB / ID: 4xvp
TitleX-ray structure of bGFP-C / EGFP complex
Components
  • BGFP-C
  • Green fluorescent protein
KeywordsPROTEIN BINDING / ALPHAREP SCAFFOLD / COMPLEX / EGFP / PROTEIN ENGINEERING / HEAT-LIKE REPEAT / FLUORESCENT PROTEIN
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
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChevrel, A. / Urvoas, A. / Li de la Sierra-Gallay, I. / Van Tilbeurgh, H. / Minard, P. / Valerio-Lepiniec, M.
CitationJournal: Biosci.Rep. / Year: 2015
Title: Specific GFP-binding artificial proteins ( alpha Rep): a new tool for in vitro to live cell applications.
Authors: Chevrel, A. / Urvoas, A. / de la Sierra-Gallay, I.L. / Aumont-Nicaise, M. / Moutel, S. / Desmadril, M. / Perez, F. / Gautreau, A. / van Tilbeurgh, H. / Minard, P. / Valerio-Lepiniec, M.
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: BGFP-C
E: BGFP-C
F: BGFP-C


Theoretical massNumber of molelcules
Total (without water)148,4906
Polymers148,4906
Non-polymers00
Water00
1
A: Green fluorescent protein
D: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-6 kcal/mol
Surface area16260 Å2
MethodPISA
2
B: Green fluorescent protein
E: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-7 kcal/mol
Surface area16510 Å2
MethodPISA
3
C: Green fluorescent protein
F: BGFP-C


Theoretical massNumber of molelcules
Total (without water)49,4972
Polymers49,4972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-6 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.520, 71.550, 179.200
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23B
14A
24C
15B
25C
16B
26C
17D
27E
18D
28F
19E
29F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA2 - 6423 - 85
21SERSERLEULEUBB2 - 6423 - 85
12SERSERLEULEUAA2 - 6423 - 85
22SERSERLEULEUCC2 - 6423 - 85
13VALVALLEULEUAA68 - 23187 - 250
23VALVALLEULEUBB68 - 23187 - 250
14VALVALLEULEUAA68 - 23187 - 250
24VALVALLEULEUCC68 - 23187 - 250
15SERSERLEULEUBB2 - 6423 - 85
25SERSERLEULEUCC2 - 6423 - 85
16VALVALLEULEUBB68 - 23187 - 250
26VALVALLEULEUCC68 - 23187 - 250
17HISHISLYSLYSDD9 - 1669 - 166
27HISHISLYSLYSEE9 - 1669 - 166
18HISHISLYSLYSDD9 - 1669 - 166
28HISHISLYSLYSFF9 - 1669 - 166
19HISHISLYSLYSEE9 - 1669 - 166
29HISHISLYSLYSFF9 - 1669 - 166

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein Green fluorescent protein


Mass: 30641.279 Da / Num. of mol.: 3 / Mutation: F64L, S65T, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: PQE81L / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Protein BGFP-C


Mass: 18855.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PLASMID / Details (production host): PQE81L / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 50 mM tricine pH 6.9, 25% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→46.7 Å / Num. obs: 17746 / % possible obs: 96.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.85
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.03 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS13-Jan-2015data reduction
XSCALE13-Jan-2015data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EGFP PDB entry 1JBZ, 6-helix motif from alphaRep4 PDB entry 3LTJ
Resolution: 3.4→46.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.867 / SU B: 43.77 / SU ML: 0.666 / Cross valid method: THROUGHOUT / ESU R Free: 0.752 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 888 5 %RANDOM
Rwork0.20918 ---
obs0.21327 16858 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.154 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å26.92 Å2
2---3.86 Å20 Å2
3---2.54 Å2
Refinement stepCycle: 1 / Resolution: 3.4→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 0 0 9144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199318
X-RAY DIFFRACTIONr_bond_other_d0.0050.028958
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.97612558
X-RAY DIFFRACTIONr_angle_other_deg0.982320670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39951146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92524.797444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.268151665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881554
X-RAY DIFFRACTIONr_chiral_restr0.0680.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210488
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022034
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.36711.3414611
X-RAY DIFFRACTIONr_mcbond_other9.36711.344610
X-RAY DIFFRACTIONr_mcangle_it14.46116.9935748
X-RAY DIFFRACTIONr_mcangle_other14.45916.9935749
X-RAY DIFFRACTIONr_scbond_it9.26912.1564706
X-RAY DIFFRACTIONr_scbond_other9.26812.1574707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.91117.9096810
X-RAY DIFFRACTIONr_long_range_B_refined19.69789.83710547
X-RAY DIFFRACTIONr_long_range_B_other19.69689.84210548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A30920.1
12B30920.1
21A31390.09
22C31390.09
31A96770.07
32B96770.07
41A96750.07
42C96750.07
51B31780.08
52C31780.08
61B96120.08
62C96120.08
71D102420.06
72E102420.06
81D102230.06
82F102230.06
91E102200.05
92F102200.05
LS refinement shellResolution: 3.396→3.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 46 -
Rwork0.397 876 -
obs--70.92 %

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