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- PDB-4xl5: X-ray structure of bGFP-A / EGFP complex -

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Basic information

Entry
Database: PDB / ID: 4xl5
TitleX-ray structure of bGFP-A / EGFP complex
Components
  • Green fluorescent protein
  • bGFP-A
KeywordsPROTEIN BINDING / AlphaRep Scaffold / Complex / EGFP / PROTEIN ENGINEERING / HEAT-LIKE REPEAT
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: 2 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 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
C: bGFP-A


Theoretical massNumber of molelcules
Total (without water)59,3362
Polymers59,3362
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 45.980, 74.890
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein


Mass: 30641.279 Da / Num. of mol.: 1
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-A


Mass: 28694.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PQE81L / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.05M MgAc, 0.1M NaAc, 5%-15% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→39.2 Å / Num. obs: 33143 / % possible obs: 98.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSJanuary 10, 2014data reduction
XSCALEJanuary 10, 2014data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBZ, 3LTJ

1jbz

3ltj


Resolution: 2→39.18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.62 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26799 1657 5 %RANDOM
Rwork0.20477 ---
obs0.208 31479 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.121 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0.66 Å2
2--4.54 Å20 Å2
3----4.3 Å2
Refinement stepCycle: 1 / Resolution: 2→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3687 0 0 103 3790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193754
X-RAY DIFFRACTIONr_bond_other_d0.0010.023657
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9845070
X-RAY DIFFRACTIONr_angle_other_deg0.83238432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26224.713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25315664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7961525
X-RAY DIFFRACTIONr_chiral_restr0.0890.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
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_it3.5644.6191881
X-RAY DIFFRACTIONr_mcbond_other3.5574.6171880
X-RAY DIFFRACTIONr_mcangle_it4.8036.9172346
X-RAY DIFFRACTIONr_mcangle_other4.8046.922347
X-RAY DIFFRACTIONr_scbond_it4.5285.1171873
X-RAY DIFFRACTIONr_scbond_other4.5275.1191874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8317.4622725
X-RAY DIFFRACTIONr_long_range_B_refined8.38337.1414353
X-RAY DIFFRACTIONr_long_range_B_other8.37237.124330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 119 -
Rwork0.385 2263 -
obs--97.26 %

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