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- PDB-4v3q: Designed armadillo repeat protein with 4 internal repeats, 2nd ge... -

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Basic information

Entry
Database: PDB / ID: 4v3q
TitleDesigned armadillo repeat protein with 4 internal repeats, 2nd generation C-cap and 3rd generation N-cap.
ComponentsYIII_M4_AII
KeywordsDE NOVO PROTEIN / PROTEIN ENGINEERING / REPEAT PROTEIN / ARMADILLO REPEAT
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: 1.8 Å
AuthorsReichen, C. / Madhurantakam, C. / Pluckthun, A. / Mittl, P.
CitationJournal: Acta Crystallogr D Struct Biol / 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.
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 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine / reflns_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _reflns_shell.Rmerge_I_obs
Revision 1.4Jan 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_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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_M4_AII
B: YIII_M4_AII
C: YIII_M4_AII
D: YIII_M4_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,79422
Polymers104,9684
Non-polymers82518
Water11,782654
1
A: YIII_M4_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,65510
Polymers26,2421
Non-polymers4139
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YIII_M4_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4144
Polymers26,2421
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: YIII_M4_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4025
Polymers26,2421
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: YIII_M4_AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3223
Polymers26,2421
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.498, 96.498, 96.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
YIII_M4_AII


Mass: 26242.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM ION (CA): FROM CRYSTALLIZATION BUFFER GLYCEROL (GOL): CRYOPROTECTANT

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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: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE
Crystal growDetails: 25 % PEG 2KMME 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: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→96.34 Å / Num. obs: 93024 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4db6

4db6


Resolution: 1.8→96.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.523 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 4660 5 %RANDOM
Rwork0.18933 ---
obs0.19168 88364 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→96.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7346 0 28 654 8028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197611
X-RAY DIFFRACTIONr_bond_other_d0.0020.027346
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.96510378
X-RAY DIFFRACTIONr_angle_other_deg0.955316953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69351015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31828.575365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.656151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.999154
X-RAY DIFFRACTIONr_chiral_restr0.1140.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219133
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021571
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_it1.5731.8144018
X-RAY DIFFRACTIONr_mcbond_other1.5681.8144017
X-RAY DIFFRACTIONr_mcangle_it2.2832.7115047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6752.2113593
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 365 -
Rwork0.309 6526 -
obs--100 %
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)
10.2714-0.03760.06161.6052-0.11330.58610.0144-0.09310.01910.24180.0882-0.3621-0.04870.0775-0.10260.07880.0029-0.06410.0547-0.04880.12128.395534.587712.708
20.29950.0314-0.03491.5805-0.14730.63160.01020.0956-0.0292-0.23960.0877-0.35970.05690.0811-0.09790.0743-0.00450.06360.0505-0.04940.12198.3921.1189-13.5814
30.84250.35580.03310.4633-0.06051.13060.1754-0.1081-0.01040.21840.15810.18440.0371-0.3077-0.33350.13620.04360.04220.20340.19990.2164-21.356725.031413.9108
40.8308-0.3643-0.06890.5068-0.03841.10010.16840.10620.0101-0.22540.16380.1906-0.0299-0.303-0.33220.1369-0.0435-0.04260.20170.19970.216-21.348430.5698-14.7201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 250
2X-RAY DIFFRACTION2B4 - 250
3X-RAY DIFFRACTION3C4 - 248
4X-RAY DIFFRACTION4D4 - 247

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