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- PDB-3a4f: Crystal Structure of Human Transthyretin (E54K) -

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Basic information

Entry
Database: PDB / ID: 3a4f
TitleCrystal Structure of Human Transthyretin (E54K)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / BETA BARREL / Amyloid / Amyloidosis / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Neuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A / THYROXINE
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMiyata, M. / Sato, T. / Nakamura, T. / Ikemizu, S. / Yamagata, Y. / Kai, H.
CitationJournal: Biochemistry / Year: 2010
Title: Role of the glutamic acid 54 residue in transthyretin stability and thyroxine binding
Authors: Miyata, M. / Sato, T. / Mizuguchi, M. / Nakamura, T. / Ikemizu, S. / Nabeshima, Y. / Susuki, S. / Suwa, Y. / Morioka, H. / Ando, Y. / Suico, M.A. / Shuto, T. / Koga, T. / Yamagata, Y. / Kai, H.
History
DepositionJul 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1118
Polymers27,5552
Non-polymers5576
Water2,324129
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,22316
Polymers55,1104
Non-polymers1,11312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6280 Å2
ΔGint-44 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.203, 42.466, 64.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-175-

HOH

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Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.427 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED REFERENCE 96 IN THE DATABASE TTHY_HUMAN (UNIPROTKB/SWISS-PROT P02766). E54K ...THE SEQUENCE IS BASED REFERENCE 96 IN THE DATABASE TTHY_HUMAN (UNIPROTKB/SWISS-PROT P02766). E54K IS VARIANT OF TTHY_HUMAN.

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 200mM citrate, 3M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 16692 / Rmerge(I) obs: 0.064 / Net I/σ(I): 45.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMZ

1bmz


Resolution: 1.99→35.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.601 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22322 842 5.1 %RANDOM
Rwork0.17164 ---
obs0.17418 15800 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.415 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.99→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 35 129 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221863
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.962533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72623.51474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11115284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.395158
X-RAY DIFFRACTIONr_chiral_restr0.1820.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211390
X-RAY DIFFRACTIONr_mcbond_it1.381.51154
X-RAY DIFFRACTIONr_mcangle_it2.52921873
X-RAY DIFFRACTIONr_scbond_it4.0823709
X-RAY DIFFRACTIONr_scangle_it6.584.5660
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 65 -
Rwork0.163 1149 -
obs--100 %
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)
11.61720.507-0.16441.5594-0.06170.6657-0.0444-0.04890.01280.0554-0.0430.15910.00760.03210.0875-0.0587-0.0040.0099-0.11740.0194-0.0674-13.191-0.605-5.887
22.1602-0.58530.68181.435-0.37760.9192-0.03230.0721-0.103-0.0636-0.0340.1021-0.05020.02350.0662-0.0592-0.0053-0.008-0.12290.0115-0.0853-12.674-3.037-25.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 125
2X-RAY DIFFRACTION2B10 - 124

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