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- PDB-4v3o: Designed armadillo repeat protein with 5 internal repeats, 2nd ge... -

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Basic information

Entry
Database: PDB / ID: 4v3o
TitleDesigned armadillo repeat protein with 5 internal repeats, 2nd generation C-cap and 3rd generation N-cap.
ComponentsYIII_M5_AII
KeywordsDE NOVO PROTEIN / ROTEIN ENGINEERING / REPEAT PROTEIN / ARMADILLO REPEAT
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha / ACETATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReichen, C. / Madhurantakam, C. / Pluckthun, A. / Mittl, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Structures of Designed Armadillo-Repeat Proteins Show Propagation of Inter-Repeat Interface Effects
Authors: Reichen, C. / Madhurantakam, C. / Hansen, S. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.E.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: YIII_M5_AII
B: YIII_M5_AII
C: YIII_M5_AII
D: YIII_M5_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,73217
Polymers122,1924
Non-polymers54013
Water13,818767
1
A: YIII_M5_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7085
Polymers30,5481
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YIII_M5_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7486
Polymers30,5481
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YIII_M5_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6283
Polymers30,5481
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YIII_M5_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6473
Polymers30,5481
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.586, 102.586, 111.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 4 - 289 / Label seq-ID: 1 - 286

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22DD

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-6.0E-5, -1, 0.000182), (-1, 6.0E-5, 0.000173), (-0.000173, -0.000182, -1)-51.30059, -51.29653, 45.45289

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Components

#1: Protein
YIII_M5_AII


Mass: 30548.010 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: NON BIOLOGICAL SEQUENCE / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM ION (CA): FROM CRYSTALLIZATION BUFFER ACETATE ION (ACT): CRYOPROTECTANT
Sequence detailsARTIFICIAL CONSTRUCT

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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: 48.58 % / Description: NONE
Crystal growDetails: 15 % PEG 4000 0.2 M CA-ACETATE 0.1 M NA-ACETATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→55.55 Å / Num. obs: 76669 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.6 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DB6

4db6


Resolution: 2→111.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.584 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22426 3859 5 %RANDOM
Rwork0.16786 ---
obs0.17065 72765 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 2→111.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8573 0 16 767 9356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198740
X-RAY DIFFRACTIONr_bond_other_d0.0020.028511
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.96311915
X-RAY DIFFRACTIONr_angle_other_deg0.982319585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38951162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19928.631409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.146151493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.042154
X-RAY DIFFRACTIONr_chiral_restr0.0980.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110451
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021817
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_it2.4662.8864637
X-RAY DIFFRACTIONr_mcbond_other2.4642.8854635
X-RAY DIFFRACTIONr_mcangle_it3.4994.3095799
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.893.54103
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2515loose positional0.065
12B2515loose positional0.065
21C2547loose positional0.045
22D2547loose positional0.045
11A1647tight thermal0.740.5
12B1647tight thermal0.740.5
21C1673tight thermal0.910.5
22D1673tight thermal0.910.5
11A2515loose thermal0.9710
12B2515loose thermal0.9710
21C2547loose thermal1.3110
22D2547loose thermal1.3110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 257 -
Rwork0.268 5106 -
obs--92.8 %
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)
10.14320.18820.00580.26850.03470.2187-0.0044-0.01640.00340.0014-0.0115-0.00780.05750.01540.01590.01850.00870.0070.016-0.0010.0155-23.5238-40.863937.1021
20.28830.21270.03170.1724-0.00390.2215-0.0075-0.0037-0.0125-0.0149-0.0117-0.00070.00940.05350.01920.01760.0091-0.00020.01650.00620.0163-10.4315-27.7698.3585
30.32720.4290.13150.6620.04510.2496-0.06290.06810.0299-0.02220.10220.0654-0.0830.0083-0.03930.0463-0.00220.00410.01840.00940.0158-32.4436-6.779636.8619
40.66570.4120.06420.3090.13220.21610.11-0.0220.07130.0695-0.06640.02830.0099-0.074-0.04370.0209-0.00290.01210.0490.00710.0201-44.2573-18.73668.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 292
2X-RAY DIFFRACTION2A4 - 292
3X-RAY DIFFRACTION3C4 - 291
4X-RAY DIFFRACTION4D4 - 289

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