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- PDB-5tvd: Crystal structure of Tm16 -

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Basic information

Entry
Database: PDB / ID: 5tvd
TitleCrystal structure of Tm16
ComponentsTm16
KeywordsUNKNOWN FUNCTION / phosphatidylethanolamine-binding protein
Function / homology
Function and homology information


Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesTrichuris muris (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.734 Å
AuthorsAsojo, O.A.
CitationJournal: J Parasitol Res / Year: 2017
Title: Identification, Characterization, and Structure of Tm16 from Trichuris muris.
Authors: Liu, Z. / Kelleher, A. / Tabb, S. / Wei, J. / Pollet, J. / Hotez, P.J. / Bottazzi, M.E. / Zhan, B. / Asojo, O.A.
History
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 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: Tm16


Theoretical massNumber of molelcules
Total (without water)21,3721
Polymers21,3721
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.970, 31.700, 63.750
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

21A-369-

HOH

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Components

#1: Protein Tm16 / Uncharacterized protein


Mass: 21371.855 Da / Num. of mol.: 1 / Fragment: UNP residues 25-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichuris muris (invertebrata) / Production host: Pichia (fungus) / References: UniProt: A0A0N5DEJ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22 mg/ml Tm16 in 5mM Bis(2-hydroxyethyl)aminotris(hydroxymethyl)methane pH 6.5 Buffer 0.1 M HEPES pH 7.5, 10% (v/v) isopropanol, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HR / Detector: IMAGE PLATE / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.734→19.93 Å / Num. obs: 17974 / % possible obs: 99.25 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.04017 / Net I/av σ(I): 10.05 / Net I/σ(I): 10.05
Reflection shellResolution: 1.734→1.796 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1777 / Mean I/σ(I) obs: 3.58 / CC1/2: 0.895 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11rc2_2531: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BD9

1bd9


Resolution: 1.734→19.928 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.95
RfactorNum. reflection% reflection
Rfree0.1982 964 5.39 %
Rwork0.168 --
obs0.1696 17884 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.734→19.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 0 244 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061459
X-RAY DIFFRACTIONf_angle_d0.8221985
X-RAY DIFFRACTIONf_dihedral_angle_d3.106854
X-RAY DIFFRACTIONf_chiral_restr0.055209
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7341-1.82540.25891400.2192360X-RAY DIFFRACTION99
1.8254-1.93970.23681510.18782382X-RAY DIFFRACTION100
1.9397-2.08930.23331390.17612400X-RAY DIFFRACTION99
2.0893-2.29930.19951270.16942412X-RAY DIFFRACTION99
2.2993-2.63140.21361270.1782418X-RAY DIFFRACTION100
2.6314-3.31280.19481440.16412427X-RAY DIFFRACTION100
3.3128-19.9290.16251360.152521X-RAY DIFFRACTION99

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