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- PDB-3ma5: Crystal structure of the tetratricopeptide repeat domain protein ... -

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Basic information

Entry
Database: PDB / ID: 3ma5
TitleCrystal structure of the tetratricopeptide repeat domain protein Q2S6C5_SALRD from Salinibacter ruber. Northeast Structural Genomics Consortium Target SrR115c.
ComponentsTetratricopeptide repeat domain protein
Keywordsstructural genomics / unknown function / Tetratricopeptide repeat domain protein / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Tetratricopeptide repeat domain protein
Similarity search - Component
Biological speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the tetratricopeptide repeat domain protein Q2S6C5_SALRD from Salinibacter ruber.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetratricopeptide repeat domain protein
B: Tetratricopeptide repeat domain protein
C: Tetratricopeptide repeat domain protein
D: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)46,4744
Polymers46,4744
Non-polymers00
Water1448
1
A: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)11,6191
Polymers11,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)11,6191
Polymers11,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)11,6191
Polymers11,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)11,6191
Polymers11,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.360, 84.360, 227.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsDimer according to gel filtration

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Components

#1: Protein
Tetratricopeptide repeat domain protein


Mass: 11618.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinibacter ruber (bacteria) / Strain: HAMAP DSM 13855 / Gene: SRU_0103 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q2S6C5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7
Details: 45-60% PEG 400, 0.03-0.05M potassium chloride, 0.1M Bis-Tris, pH 7.0, microbatch under Paraffin oil, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97869 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 22394 / Num. obs: 22372 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 59.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 22 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 3.47 / Num. unique all: 2244 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KCL

2kcl


Resolution: 2.8→44.885 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Stereochemistry target values: ML
Details: There are four molecules (two dimers) in AU. The fourth molecule (D) has very bad defined electron density and was not found by MR. Based on the partial electron density and dimer structure ...Details: There are four molecules (two dimers) in AU. The fourth molecule (D) has very bad defined electron density and was not found by MR. Based on the partial electron density and dimer structure C-terminal part (78-145) of molecule D was built; however B-factor for D molecule is higher than for A-C molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1089 4.89 %RANDOM
Rwork0.2391 ---
obs0.2408 22291 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.224 Å2 / ksol: 0.333 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→44.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 8 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092750
X-RAY DIFFRACTIONf_angle_d1.4883720
X-RAY DIFFRACTIONf_dihedral_angle_d23.6081009
X-RAY DIFFRACTIONf_chiral_restr0.112406
X-RAY DIFFRACTIONf_plane_restr0.007500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7992-2.92650.34321750.34222629X-RAY DIFFRACTION100
2.9265-3.08080.40291270.30872621X-RAY DIFFRACTION100
3.0808-3.27380.30771220.28492687X-RAY DIFFRACTION100
3.2738-3.52640.27611550.252638X-RAY DIFFRACTION100
3.5264-3.88110.3921270.24492647X-RAY DIFFRACTION100
3.8811-4.44230.23721520.21162652X-RAY DIFFRACTION100
4.4423-5.59520.23581290.22242665X-RAY DIFFRACTION100
5.5952-44.89040.24571020.22712663X-RAY DIFFRACTION99

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