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- PDB-2fo7: Crystal structure of an 8 repeat consensus TPR superhelix (trigon... -

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Basic information

Entry
Database: PDB / ID: 2fo7
TitleCrystal structure of an 8 repeat consensus TPR superhelix (trigonal crystal form)
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: 2.3 Å
AuthorsKajander, T. / Cortajarena, A.L. / 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. / Main, E. / Mochrie, S. / Regan, L.
History
DepositionJan 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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
Remark 400COMPOUND THE COMPLETE CRYSTALLIZED SEQUENCE IS TWICE LONGER THAN THE SUBMITTED ONE. THE LINK RECORD ...COMPOUND THE COMPLETE CRYSTALLIZED SEQUENCE IS TWICE LONGER THAN THE SUBMITTED ONE. THE LINK RECORD IS PROVIDED TO CONNECT THE DEPOSITED PART OF THE SEQUENCE WITH THE SECOND PART OF THE COMPLETE CRYSTALLIZED 8-REPEAT MOLECULE THAT CAN BE GENERATED FROM THE DEPOSITED COORDINATES USING THE MATRIX PROVIDED IN REMARK 350.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE MOLECULE REPRESENTS A PSEUDO-INFINITE FIBER. THE SECOND PART OF THE COMPLETE COVALENT MOLECULE CAN BE GENERATED BY APPLYING THE MATRIX PROVIDED IN REMARK 350.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYNTHETIC CONSENSUS TPR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3763
Polymers16,1511
Non-polymers2252
Water1448
1
A: SYNTHETIC CONSENSUS TPR PROTEIN
hetero molecules

A: SYNTHETIC CONSENSUS TPR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7526
Polymers32,3022
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)68.550, 68.550, 67.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the individual molecule can be generated by the two fold crystallographic operator -X,Y-X,1/3-Z, with translations 1, 1, 0. which is equal to use of the following transformations: A 1.00000 0.00000 0.00000 0.00 A 0.00000 1.00000 0.00000 0.00 A 0.00000 0.00000 1.00000 0.00 B -1.00000 0.00000 0.00000 68.550 B -1.00000 1.00000 0.00000 68.550 B 0.00000 0.00000 -1.00000 22.410

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Components

#1: Protein SYNTHETIC CONSENSUS TPR PROTEIN


Mass: 16151.237 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.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% MPD, 10 mM CDCL2, 100 mM NA-ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, 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 22, 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
ReflectionAv σ(I) over netI: 17.2 / Number: 53603 / Rmerge(I) obs: 0.041 / Χ2: 1.13 / D res high: 2.28 Å / D res low: 50 Å / Num. obs: 15329 / % possible obs: 95
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
2.282.3696861.110.3250.985
2.362.46147189.910.3520.921
2.462.57157799.110.2890.91
2.572.7160199.910.210.967
2.72.87162610010.1260.961
2.873.09164510010.0811.091
3.093.41159810010.0581.227
3.413.9160610010.0381.368
3.94.91163099.910.031.373
4.915016079910.0241.239
ReflectionResolution: 2.28→50 Å / Num. obs: 15329 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.127 / Net I/σ(I): 17.2
Reflection shellResolution: 2.28→2.36 Å / % possible obs: 61.1 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 968 / Χ2: 0.985 / % possible all: 61.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 30 Å / FOM : 0.31 / Reflection: 6260
Phasing MAD set siteAtom type symbol: Cd / B iso: 41.432 / Fract x: 0.771 / Fract y: 0.692 / Fract z: 0.062 / Occupancy: 0.733
Phasing MAD shell
Resolution (Å)FOM Reflection
8.87-300.3338
5.64-8.870.38564
4.43-5.640.4700
3.76-4.430.41812
3.32-3.760.37884
3.01-3.320.3958
2.77-3.010.221007
2.58-2.770.15997
Phasing dmFOM : 0.55 / FOM acentric: 0.56 / FOM centric: 0.51 / Reflection: 6261 / Reflection acentric: 5379 / Reflection centric: 882
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-29.2510.870.90.83313204109
4.5-7.10.830.870.69910724186
3.6-4.50.790.820.621101929172
3.1-3.60.60.620.461057933124
2.7-3.10.380.390.2718411648193
2.5-2.70.210.220.16103994198

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 676 4.3 %random
Rwork0.266 ---
obs0.266 14271 90.7 %-
all-14271 --
Solvent computationBsol: 69.783 Å2
Displacement parametersBiso mean: 60.345 Å2
Baniso -1Baniso -2Baniso -3
1--8.57 Å2-7.901 Å20 Å2
2---8.57 Å20 Å2
3---17.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 2 8 1055
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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