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- PDB-3uaf: Crystal Structure of a TTR-52 mutant of C. elegans -

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Basic information

Entry
Database: PDB / ID: 3uaf
TitleCrystal Structure of a TTR-52 mutant of C. elegans
ComponentsTTR-52
KeywordsPROTEIN BINDING / beta barrel/sandwich / cell engulfment / secreted
Function / homology
Function and homology information


recognition of apoptotic cell / aminophospholipid transport / scavenger receptor binding / apoptotic process involved in development / phosphatidylserine binding / extracellular vesicle / protein-macromolecule adaptor activity / cell surface / protein homodimerization activity
Similarity search - Function
Immunoglobulin-like - #3330 / Transthyretin-like / Transthyretin-like family / Transthyretin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transthyretin-like protein 52
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.01 Å
AuthorsKang, Y.Y. / Zhao, D.F. / Liang, H.H. / Liu, B. / Liu, Q.W. / Wang, X.C. / Liu, Y.F.
CitationJournal: Genes Dev. / Year: 2012
Title: Structural study of TTR-52 reveals the mechanism by which a bridging molecule mediates apoptotic cell engulfment
Authors: Kang, Y.Y. / Zhao, D.F. / Liang, H.H. / Liu, B. / Zhang, Y. / Liu, Q.W. / Wang, X.C. / Liu, Y.F.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TTR-52


Theoretical massNumber of molelcules
Total (without water)13,0431
Polymers13,0431
Non-polymers00
Water2,126118
1
A: TTR-52

A: TTR-52


Theoretical massNumber of molelcules
Total (without water)26,0852
Polymers26,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.321, 33.368, 49.265
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

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Components

#1: Protein TTR-52


Mass: 13042.625 Da / Num. of mol.: 1 / Fragment: residues 21-135 / Mutation: E50A,D51A,S52A,L53A,P54A,L55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: G5ED35
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.5
Details: 0.2M ammonium sulfate, 0.1M soldium acetate, 35% PEGME2000, pH 4.5, EVAPORATION, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
ROTATING ANODERIGAKU FR-E SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEAug 8, 2007
RIGAKU RAXIS IV++2IMAGE PLATESep 10, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI200SINGLE WAVELENGTHMx-ray1
2SI200SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 7360 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.23 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.01-2.081,297.4
2.08-2.171,298
2.17-2.261,298.5
2.26-2.381,298.5
2.38-2.531,299.2
2.53-2.731,299.1
2.73-31,299.5
3-3.441,2100
3.44-4.331,2100
4.33-501,299.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.01→33.655 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8704 / SU ML: 0.22 / σ(F): 0 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 713 9.69 %RANDOM
Rwork0.1728 6647 --
obs0.1776 7360 98.7 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.481 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 69.79 Å2 / Biso mean: 21.2378 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.9106 Å20 Å2-2.2315 Å2
2---0.842 Å2-0 Å2
3---1.7526 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 0 118 1033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007942
X-RAY DIFFRACTIONf_angle_d1.1051286
X-RAY DIFFRACTIONf_chiral_restr0.078142
X-RAY DIFFRACTIONf_plane_restr0.005170
X-RAY DIFFRACTIONf_dihedral_angle_d13.065339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0101-2.16530.251430.18141294143797
2.1653-2.38310.22441190.16461317143698
2.3831-2.72790.23651310.17631339147099
2.7279-3.43630.24511540.178813271481100
3.4363-33.65970.19341660.167913701536100

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