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- PDB-4d49: Crystal structure of computationally designed armadillo repeat pr... -

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Basic information

Entry
Database: PDB / ID: 4d49
TitleCrystal structure of computationally designed armadillo repeat proteins for modular peptide recognition.
Components
  • ARMADILLO REPEAT PROTEIN ARM00027
  • POLY ARG DECAPEPTIDE
KeywordsDE NOVO PROTEIN/PEPTIDE / DE NOVO PROTEIN-PEPTIDE COMPLEX
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / ARGININE
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 27, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 ARM00027
B: ARMADILLO REPEAT PROTEIN ARM00027
C: POLY ARG DECAPEPTIDE
D: POLY ARG DECAPEPTIDE
E: ARMADILLO REPEAT PROTEIN ARM00027
F: ARMADILLO REPEAT PROTEIN ARM00027
G: POLY ARG DECAPEPTIDE
H: POLY ARG DECAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,11410
Polymers109,7648
Non-polymers3502
Water4,288238
1
A: ARMADILLO REPEAT PROTEIN ARM00027
B: ARMADILLO REPEAT PROTEIN ARM00027
C: POLY ARG DECAPEPTIDE
D: POLY ARG DECAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0575
Polymers54,8824
Non-polymers1751
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: ARMADILLO REPEAT PROTEIN ARM00027
F: ARMADILLO REPEAT PROTEIN ARM00027
G: POLY ARG DECAPEPTIDE
H: POLY ARG DECAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0575
Polymers54,8824
Non-polymers1751
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.570, 51.730, 107.610
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22F
13B
23E
14A
24F
15A
25E
16F
26E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 12 - 249 / Label seq-ID: 5 - 242

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12BB
22FF
13BB
23EE
14AA
24FF
15AA
25EE
16FF
26EE

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ARMADILLO REPEAT PROTEIN ARM00027


Mass: 25851.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COMPUTATIONALLY DESIGNED ARMADILLO REPEAT PROTEIN IN COMPLEX WITH A PEPTIDE
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DE NOVO DESIGNED PROTEIN / Plasmid: YIII_(DQ_V1)4_C(PAF) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Protein/peptide
POLY ARG DECAPEPTIDE


Mass: 1589.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: DE NOVO DESIGNED PROTEIN / Plasmid: YIII_(DQ_V1)4_C(PAF) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.39 Å3/Da / Density % sol: 48.48 % / Description: DATA WERE COLLECTED USING THE ROTATION METHOD
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED AT PH 8.5 / 0.2M MAGNESIUM CHLORIDE / 0.1 M TRIS HCL / 10 % W/V PEG 8000 / 10 % W/V PEG 1000. PRIOR TO CRYSTALLIZATION, 1.5 MOLAR EXCESS OF PEPTIDE (RR)5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11-h,-k,l20.495
ReflectionResolution: 2.1→20 Å / Num. obs: 106706 / % possible obs: 95.7 % / Observed criterion σ(I): 1.37 / Redundancy: 2.26 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.01
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.32 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.37 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARM00016

Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.082 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25454 2763 4.9 %RANDOM
Rwork0.20088 ---
obs0.20357 53936 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.459 Å2
Baniso -1Baniso -2Baniso -3
1-22.4 Å20 Å2-1.13 Å2
2--12.78 Å20 Å2
3----35.18 Å2
Refinement stepCycle: LAST / Resolution: 2.09→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 22 238 7812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197657
X-RAY DIFFRACTIONr_bond_other_d0.0080.027743
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.97610339
X-RAY DIFFRACTIONr_angle_other_deg1.416317800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20226.932365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.911151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9791544
X-RAY DIFFRACTIONr_chiral_restr0.0980.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028833
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021551
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_it3.3413.2733956
X-RAY DIFFRACTIONr_mcbond_other3.343.2733955
X-RAY DIFFRACTIONr_mcangle_it5.0084.8994929
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3753.5733701
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B146880.11
12A146880.11
21B146540.11
22F146540.11
31B146670.11
32E146670.11
41A147560.1
42F147560.1
51A148050.1
52E148050.1
61F147990.1
62E147990.1
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 186 -
Rwork0.245 3595 -
obs--90.02 %
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)
10.19980.055-0.12760.029-0.0180.4778-0.02380.00910.01970.0117-0.0187-0.00020.01910.00540.04250.081-0.0082-0.01660.0428-0.00270.188920.9446-2.132513.0655
20.0557-0.0528-0.13380.37220.1260.3494-0.0173-0.0192-0.0215-0.0019-0.0910.03050.01280.04350.10830.05430.0356-0.0340.0975-0.00050.148131.7752-9.414943.4601
30.56520.8831-0.56412.9575-1.59040.88170.2611-0.2175-0.1060.0471-0.20540.2168-0.09450.1632-0.05570.1841-0.1192-0.1350.1080.04290.163523.6944-11.534938.4575
40.41710.2282-0.94210.3029-1.29825.5713-0.16140.0073-0.0064-0.073-0.0507-0.04560.29870.23110.21210.118-0.00570.00290.02750.00060.146220.4232-11.04410.5252
50.056-0.05810.11820.24-0.31940.8450.0176-0.01320.0827-0.005-0.1146-0.08010.0573-0.01860.0970.0202-0.0290.00020.14020.00720.1762-23.73921.993840.6357
60.01220.03720.05860.34430.07460.4087-0.01-0.0032-0.0018-0.0187-0.0508-0.0062-0.00270.04240.06080.0630.01640.00710.04610.00860.1932-13.0299.236610.3748
70.65540.4065-0.84090.5972-1.30112.84080.0689-0.01420.1662-0.05220.01210.04620.1301-0.0276-0.0810.1051-0.02110.00680.0159-0.01340.1637-21.054610.71815.874
81.7498-0.4794-1.72050.19930.87324.13470.156-0.0215-0.3852-0.0015-0.0450.0120.1991-0.2681-0.1110.205-0.07230.01340.04010.03760.2857-24.774210.78843.119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B12 - 249
2X-RAY DIFFRACTION2A12 - 249
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D2 - 10
5X-RAY DIFFRACTION5F12 - 249
6X-RAY DIFFRACTION6E12 - 249
7X-RAY DIFFRACTION7G1 - 9
8X-RAY DIFFRACTION8H2 - 10

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