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- PDB-1na0: Design of Stable alpha-Helical Arrays from an Idealized TPR Motif -

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Basic information

Entry
Database: PDB / ID: 1na0
TitleDesign of Stable alpha-Helical Arrays from an Idealized TPR Motif
Componentsdesigned protein CTPR3
KeywordsDE NOVO PROTEIN / design / TPR
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ACETATE ION / 1-methylethyl 1-thio-beta-D-galactopyranoside / LEAD (II) ION
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMain, E. / Xiong, Y. / Cocco, M. / D'Andrea, L. / Regan, L.
CitationJournal: Structure / Year: 2003
Title: Design of Stable alpha-Helical Arrays from an Idealized TPR Motif
Authors: Main, E. / Xiong, Y. / Cocco, M. / D'Andrea, L. / Regan, L.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: designed protein CTPR3
B: designed protein CTPR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,41614
Polymers28,7382
Non-polymers1,67712
Water2,828157
1
A: designed protein CTPR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7843
Polymers14,3691
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: designed protein CTPR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,63211
Polymers14,3691
Non-polymers1,26310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.734, 46.560, 52.517
Angle α, β, γ (deg.)90.00, 99.11, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-381-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein designed protein CTPR3


Mass: 14369.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#7: Sugar ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 167 molecules

#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, PEG 4000, MgCl2, IPTG, NaCl, pH 8., VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
210 mMTris1droppH7.5
350 mM1dropNaCl
4100 mMTris1reservoirpH8.
535 %PEG40001reservoir
60.2 M1reservoirMgCl2
710 %IPTG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→33.9 Å / Num. all: 29432 / Num. obs: 22432 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 29.6
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.82 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 33.9 Å
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.959 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21598 2953 9.1 %RANDOM
Rwork0.18271 ---
obs0.1858 29432 100 %-
all-29432 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.652 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-0.12 Å2
2---0.45 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 43 157 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212051
X-RAY DIFFRACTIONr_bond_other_d0.0020.021577
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9512787
X-RAY DIFFRACTIONr_angle_other_deg0.91533728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4465236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1390.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined0.2350.2508
X-RAY DIFFRACTIONr_nbd_other0.240.21712
X-RAY DIFFRACTIONr_nbtor_other0.0860.21014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8411.51183
X-RAY DIFFRACTIONr_mcangle_it1.49621842
X-RAY DIFFRACTIONr_scbond_it3.083868
X-RAY DIFFRACTIONr_scangle_it4.7744.5945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.686 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.324 434
Rwork0.283 4219
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)
18.38682.1609-0.89524.41190.3482.1254-0.1634-0.0398-0.1624-0.08750.0826-0.29290.05240.05740.08080.11980.0422-0.00310.1198-0.03050.037936.457-10.811.694
26.31240.6282-1.44792.9555-0.66331.7128-0.1045-0.02670.40380.09350.1571-0.195-0.08070.1124-0.05250.109-0.0029-0.00980.1186-0.02820.033230.410.02714.445
37.583-0.16651.18632.3172-2.03774.5512-0.26390.21360.8767-0.06190.1416-0.0994-0.20760.08690.12230.1279-0.004-0.03080.10960.01440.129620.1687.81412.847
410.33211.302-0.09394.65342.390716.3332-0.1419-0.27690.9477-0.02920.00580.2511-0.5267-0.36580.13610.11370.0383-0.0430.13750.03090.156410.5867.82713.55
59.69060.56651.54064.5233-0.16192.0049-0.0874-0.0457-0.1771-0.1167-0.06750.4306-0.0467-0.03790.15490.12270.05060.01020.1131-0.0040.11445.68524.43411.91
65.67970.56131.58994.92531.31861.5975-0.06580.0336-0.27380.07080.02960.58810.14320.0110.03620.11250.01920.0350.12640.04210.128351.73213.59714.964
79.2613-0.47851.62363.73751.04164.76140.07790.8189-0.6501-0.22770.04860.32250.20530.0612-0.12650.13730.0202-0.00140.1953-0.01230.109761.8465.92413.169
813.3228-2.44344.64696.8677-5.186517.36490.10550.621-0.1278-0.1332-0.06520.00990.24450.1219-0.04030.10020.02780.02740.165-0.02240.025871.546.01613.732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 407 - 40
2X-RAY DIFFRACTION2AA41 - 7441 - 74
3X-RAY DIFFRACTION3AA75 - 10875 - 108
4X-RAY DIFFRACTION4AA109 - 125109 - 125
5X-RAY DIFFRACTION5BB7 - 407 - 40
6X-RAY DIFFRACTION6BB41 - 7441 - 74
7X-RAY DIFFRACTION7BB75 - 10875 - 108
8X-RAY DIFFRACTION8BB109 - 125109 - 125
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.69 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.28

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