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- PDB-3ltj: Structure of a new family of artificial alpha helicoidal repeat p... -

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Basic information

Entry
Database: PDB / ID: 3ltj
TitleStructure of a new family of artificial alpha helicoidal repeat proteins (alpha-Rep) based on thermostable HEAT-like repeats
ComponentsAlphaRep-4
KeywordsPROTEIN BINDING / protein engineering / HEAT-like repeat
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUrvoas, A. / Guellouz, A. / Graille, M. / van Tilbeurgh, H. / Desmadril, M. / Minard, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins ( alpha Rep) based on thermostable HEAT-like repeats
Authors: Urvoas, A. / Guellouz, A. / Valerio-Lepiniec, M. / Graille, M. / Durand, D. / Desravines, D.C. / van Tilbeurgh, H. / Desmadril, M. / Minard, P.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AlphaRep-4


Theoretical massNumber of molelcules
Total (without water)22,2241
Polymers22,2241
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AlphaRep-4

A: AlphaRep-4


Theoretical massNumber of molelcules
Total (without water)44,4482
Polymers44,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2190 Å2
ΔGint-9 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.630, 85.180, 34.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

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Components

#1: Protein AlphaRep-4


Mass: 22224.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 4% MPD, 0.1M Na citrate pH 5.6, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 17826 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.27 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LTM

3ltm


Resolution: 1.8→25.744 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.852 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 891 5.01 %random
Rwork0.1741 ---
all0.1768 ---
obs0.1768 17789 97.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.556 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 87.63 Å2 / Biso mean: 25.137 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--7.433 Å20 Å20 Å2
2--3.274 Å2-0 Å2
3---4.159 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 0 140 1627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051517
X-RAY DIFFRACTIONf_angle_d0.8922051
X-RAY DIFFRACTIONf_dihedral_angle_d18.183561
X-RAY DIFFRACTIONf_chiral_restr0.061223
X-RAY DIFFRACTIONf_plane_restr0.004272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.26451460.18682757X-RAY DIFFRACTION98
1.9128-2.06040.27531430.17342735X-RAY DIFFRACTION97
2.0604-2.26760.22241440.16952729X-RAY DIFFRACTION96
2.2676-2.59550.23421460.1682794X-RAY DIFFRACTION98
2.5955-3.2690.22141530.18232891X-RAY DIFFRACTION100
3.269-25.74610.21011590.16842992X-RAY DIFFRACTION99

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