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

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Basic information

Entry
Database: PDB / ID: 3ltm
TitleStructure of a new family of artificial alpha helicoidal repeat proteins (alpha-Rep) based on thermostable HEAT-like repeats
ComponentsAlpha-Rep4
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 / MAD / Resolution: 2.15 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Alpha-Rep4
B: Alpha-Rep4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7766
Polymers46,8072
Non-polymers9694
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-19 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.440, 52.450, 83.970
Angle α, β, γ (deg.)90.00, 91.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-Rep4


Mass: 23403.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18.5% PEG 1000, 6.5% glycerol, 100 mM tricine pH8, 230 mM NaCl, 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: 0.91971, 0.9795, 0.93
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919711
20.97951
30.931
ReflectionResolution: 2.15→30 Å / Num. obs: 20242 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.446 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→19.802 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.807 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1033 5.11 %random
Rwork0.174 ---
all0.1779 ---
obs0.1779 20213 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.149 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 151.78 Å2 / Biso mean: 33.584 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.375 Å2-0 Å24.068 Å2
2---6.283 Å2-0 Å2
3---5.908 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 63 331 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072958
X-RAY DIFFRACTIONf_angle_d1.053975
X-RAY DIFFRACTIONf_dihedral_angle_d20.1881130
X-RAY DIFFRACTIONf_chiral_restr0.089429
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.26320.3111610.21322708X-RAY DIFFRACTION100
2.2632-2.40480.33721440.20632713X-RAY DIFFRACTION100
2.4048-2.59010.29911400.20792723X-RAY DIFFRACTION100
2.5901-2.850.30571540.19172726X-RAY DIFFRACTION100
2.85-3.26090.27731340.17632754X-RAY DIFFRACTION100
3.2609-4.10230.19431550.12832740X-RAY DIFFRACTION100
4.1023-19.80280.17421450.14572816X-RAY DIFFRACTION100

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