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- PDB-2avp: Crystal structure of an 8 repeat consensus TPR superhelix -

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Basic information

Entry
Database: PDB / ID: 2avp
TitleCrystal structure of an 8 repeat consensus TPR superhelix
Componentssynthetic consensus TPR protein
KeywordsDE NOVO PROTEIN / tetratricopeptide repeat / TPR / consensus protein / superhelix
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / :
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsKajander, T. / Cortajarena, A.L. / Main, E.R. / Mochrie, S. / Regan, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins.
Authors: Kajander, T. / Cortajarena, A.L. / Mochrie, S. / Regan, L.
#1: Journal: J.Am.Chem.Soc. / Year: 2005
Title: A new folding paradigm for repeat proteins
Authors: Kajander, T. / Lopez-Cortajarena, A.L. / Main, E.R. / Mochrie, S.G. / Regan, L.
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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_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 / _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

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Assembly

Deposited unit
A: synthetic consensus TPR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4543
Polymers8,2291
Non-polymers2252
Water43224
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A: synthetic consensus TPR protein
hetero molecules

A: synthetic consensus TPR protein
hetero molecules

A: synthetic consensus TPR protein
hetero molecules

A: synthetic consensus TPR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,81412
Polymers32,9154
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-1/21
crystal symmetry operation3_544-y+1/2,x-1/2,z-3/41
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Unit cell
Length a, b, c (Å)54.245, 54.245, 71.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-202-

CD

21A-206-

HOH

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Components

#1: Protein synthetic consensus TPR protein


Mass: 8228.750 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of the protein was designed and then expressed in E.coli BL21(DE3), plasmid pPROEX-HTb
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5
Details: MPD, CdCl2, NaAcetate, NaCl, pH 5.0, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.6 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.04→29.9 Å / Num. obs: 12784 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.037
Reflection shellResolution: 2.04→2.11 Å / Mean I/σ(I) obs: 7.7 / Rsym value: 0.237 / % possible all: 94.1

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Phasing

Phasing dmFOM : 0.6 / FOM acentric: 0.62 / FOM centric: 0.5 / Reflection: 6815 / Reflection acentric: 5566 / Reflection centric: 1249
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.8-29.9330.820.910.71356192164
3.6-5.80.880.930.741003725278
2.9-3.60.780.840.561201957244
2.6-2.90.650.690.411165974191
2.2-2.60.470.50.2719781721257
2-2.20.280.290.141112997115

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Processing

Software
NameVersionClassificationNB
RESOLVE2.02phasing
REFMAC5.1.24refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→29.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.529 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 690 10 %RANDOM
Rwork0.201 ---
all0.205 ---
obs0.205 6934 95.52 %-
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: 35.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.04→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms554 0 2 24 580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021564
X-RAY DIFFRACTIONr_bond_other_d0.0020.02445
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.933767
X-RAY DIFFRACTIONr_angle_other_deg1.11531034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94567
X-RAY DIFFRACTIONr_chiral_restr0.1580.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
X-RAY DIFFRACTIONr_nbd_refined0.2330.2129
X-RAY DIFFRACTIONr_nbd_other0.260.2457
X-RAY DIFFRACTIONr_nbtor_other0.0930.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3260.215
X-RAY DIFFRACTIONr_metal_ion_refined0.090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5590.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7170.26
X-RAY DIFFRACTIONr_mcbond_it3.5642338
X-RAY DIFFRACTIONr_mcangle_it4.8193523
X-RAY DIFFRACTIONr_scbond_it7.3424226
X-RAY DIFFRACTIONr_scangle_it9.2576244
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.219 52
Rwork0.221 404
all-456
Refinement TLS params.Method: refined / Origin x: 20.926 Å / Origin y: 9.2059 Å / Origin z: 60.2067 Å
111213212223313233
T0.0024 Å20.0106 Å20.0058 Å2-0.054 Å20.0136 Å2--0.0319 Å2
L0.6365 °20.414 °2-0.7904 °2-0.5119 °2-0.078 °2--0.8775 °2
S-0.0004 Å °0.0314 Å °0.0502 Å °-0.0238 Å °0.061 Å °0.0273 Å °0.0587 Å °-0.0199 Å °-0.0606 Å °
Refinement TLS groupSelection: ALL

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