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- PDB-7obi: Consensus tetratricopeptide repeat protein type RV4 -

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Basic information

Entry
Database: PDB / ID: 7obi
TitleConsensus tetratricopeptide repeat protein type RV4
ComponentsCTPR-rv4
KeywordsDE NOVO PROTEIN / CTPR / tandem-repeat protein
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsEapen, R.S. / Perez-Riba, A. / Fischer, G. / Itzhaki, L.S. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Acs Nano / Year: 2022
Title: Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix.
Authors: Synakewicz, M. / Eapen, R.S. / Perez-Riba, A. / Rowling, P.J.E. / Bauer, D. / Weissl, A. / Fischer, G. / Hyvonen, M. / Rief, M. / Itzhaki, L.S. / Stigler, J.
History
DepositionApr 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTPR-rv4
B: CTPR-rv4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3386
Polymers34,9582
Non-polymers3804
Water0
1
A: CTPR-rv4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5742
Polymers17,4791
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CTPR-rv4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7644
Polymers17,4791
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.912, 58.912, 189.517
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CTPR-rv4


Mass: 17479.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M sodium cacodylate pH 6.5, 50 % PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→51.02 Å / Num. obs: 8214 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 114.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 18.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.739 / Num. unique obs: 1143 / CC1/2: 0.778 / Rpim(I) all: 0.682 / Rrim(I) all: 1.871 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSMarch 1, 2015data reduction
Aimless0.5.4data scaling
PHASER2.8.3phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYZ

2hyz


Resolution: 3→51.02 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.423
RfactorNum. reflection% reflectionSelection details
Rfree0.271 405 4.97 %RANDOM
Rwork0.2257 ---
obs0.2278 8153 99.6 %-
Displacement parametersBiso max: 216.96 Å2 / Biso mean: 131.46 Å2 / Biso min: 103.25 Å2
Baniso -1Baniso -2Baniso -3
1--13.4392 Å20 Å20 Å2
2---13.4392 Å20 Å2
3---26.8784 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 20 0 2207
Biso mean--177.48 --
Num. residues----268
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d801SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2240HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion259SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1865SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2240HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3028HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion24.67
LS refinement shellResolution: 3→3.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.2535 11 2.7 %
Rwork0.2873 397 -
all0.2865 408 -
obs--93.55 %
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)
12.8073-1.86152.01934.7898-1.14819.54430.19010.30020.14240.1875-0.0482-0.3806-0.4750.0657-0.14190.00210.18110.185-0.21210.0014-0.0698-22.77678.092231.4484
23.72452.8799-3.16294.8848-3.31974.5767-0.41070.2256-0.3234-0.32820.2084-0.25360.7068-0.02930.20230.06560.39190.02330.1707-0.0531-0.1088-22.9662-4.83084.5252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 136
2X-RAY DIFFRACTION2{ B|* }B1 - 134

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