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- PDB-4jw2: Selection of specific protein binders for pre-defined targets fro... -

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Basic information

Entry
Database: PDB / ID: 4jw2
TitleSelection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)
Components
  • A3 artificial protein
  • bA3-2: binder of A3 protein
KeywordsDE NOVO PROTEIN/protein binding / alpha-helical proteins / Proteins engineered to bind to various partners / DE NOVO PROTEIN-protein binding complex
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuellouz, A. / Valerio-Lepiniec, M. / Urvoas, A. / Chevrel, A. / Graille, M. / Fourati-Kammoun, Z. / Desmadril, M. / van Tilbeurgh, H. / Minard, P.
CitationJournal: Plos One / Year: 2013
Title: Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep).
Authors: Guellouz, A. / Valerio-Lepiniec, M. / Urvoas, A. / Chevrel, A. / Graille, M. / Fourati-Kammoun, Z. / Desmadril, M. / van Tilbeurgh, H. / Minard, P.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A3 artificial protein
B: bA3-2: binder of A3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3585
Polymers34,1722
Non-polymers1863
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-0 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.760, 87.760, 77.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein A3 artificial protein


Mass: 11947.639 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)
#2: Protein bA3-2: binder of A3 protein


Mass: 22224.102 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% (w/v) PEG 2,000 MME, 100 mM Na acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Feb 29, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 24720 / Num. obs: 24498 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 36.05 Å2 / Rsym value: 0.048 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.566 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTM

3ltm


Resolution: 1.9→28.83 Å / Cor.coef. Fo:Fc: 0.9204 / Cor.coef. Fo:Fc free: 0.9132 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1242 5.09 %RANDOM
Rwork0.1939 ---
all0.1954 24720 --
obs0.1954 24407 --
Displacement parametersBiso mean: 48.27 Å2
Baniso -1Baniso -2Baniso -3
1--9.5317 Å20 Å20 Å2
2---9.5317 Å20 Å2
3---19.0633 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 12 146 2193
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022796HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d755SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2078HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion19.52
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2614SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2748 132 4.53 %
Rwork0.2725 2785 -
all0.2726 2917 -

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