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- PDB-4d4e: Crystal structure of computationally designed armadillo repeat pr... -

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Basic information

Entry
Database: PDB / ID: 4d4e
TitleCrystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.
ComponentsARMADILLO REPEAT PROTEIN ARM00016
KeywordsDE NOVO PROTEIN / ARMADILLO REPEAT PROTEIN
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: 2 Å
AuthorsReichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. ...Reichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. / Baker, D. / Caflisch, A. / Pluckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.
Authors: Reichen, C. / Forzani, C. / Zhou, T. / Parmeggiani, F. / Fleishman, S.J. / Mittl, P.R.E. / Madhurantakam, C. / Honegger, A. / Ewald, C. / Zerbe, O. / Baker, D. / Caflisch, A. / Pluckthun, A.
History
DepositionOct 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: ARMADILLO REPEAT PROTEIN ARM00016
B: ARMADILLO REPEAT PROTEIN ARM00016
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0245
Polymers52,7472
Non-polymers2763
Water4,504250
1
A: ARMADILLO REPEAT PROTEIN ARM00016
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4662
Polymers26,3741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARMADILLO REPEAT PROTEIN ARM00016
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5583
Polymers26,3741
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.810, 68.670, 126.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARMADILLO REPEAT PROTEIN ARM00016


Mass: 26373.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPUTATIONALLY DESIGNED ARMADILLO REPEAT PROTEIN / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DE NOVO DESIGNED PROTEIN / Plasmid: YIII_(DQ)4_C(PAF) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Description: DESIGNED ARMADILLO REPEAT PROTEIN ARM00009 WAS SOLVED BY USING AN POLY-ALA-MODEL, THAT WAS CREATED FROM THE CRYSTAL STRUCTURE OF AN N4C CONSENSUS-BASED ARMRP PDB ID 4V3Q. DATA WERE ...Description: DESIGNED ARMADILLO REPEAT PROTEIN ARM00009 WAS SOLVED BY USING AN POLY-ALA-MODEL, THAT WAS CREATED FROM THE CRYSTAL STRUCTURE OF AN N4C CONSENSUS-BASED ARMRP PDB ID 4V3Q. DATA WERE COLLECTED BY ROTATION METHOD.
Crystal growpH: 5.5
Details: PH 5.5 0.3 M NA-ACETATE/ 0.1 M NA- ACETATE/ 25 % PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.12 Å / Num. obs: 27662 / % possible obs: 88.2 % / Observed criterion σ(I): 2.3 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARM00009

Resolution: 2→39.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.588 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26342 1384 5 %RANDOM
Rwork0.18754 ---
obs0.19119 26231 88.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---1.16 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 18 250 3758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193562
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9914832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.53929.49157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96715664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.956152
X-RAY DIFFRACTIONr_chiral_restr0.1290.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212628
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.318 89 -
Rwork0.26 1537 -
obs--72.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40780.4720.17561.5732-0.23330.3132-0.0520.0222-0.06070.09380.1191-0.0742-0.0413-0.0469-0.06710.06660.0025-0.02920.01850.0040.04187.3227-19.3017-18.6557
20.4970.4568-0.57880.7846-0.37371.4434-0.07280.0316-0.12510.04110.0462-0.1896-0.02640.02230.02650.0706-0.00870.01310.0085-0.01530.061719.5604-38.3250.7028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 249
2X-RAY DIFFRACTION2B12 - 249

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