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- PDB-3a4e: Crystal structure of Human Transthyretin (E54G) -

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Basic information

Entry
Database: PDB / ID: 3a4e
TitleCrystal structure of Human Transthyretin (E54G)
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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / 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: 1.7 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 / pdbx_struct_special_symmetry / 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)27,8797
Polymers27,4112
Non-polymers4685
Water2,954164
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,75814
Polymers54,8214
Non-polymers93710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6200 Å2
ΔGint-45 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.671, 41.617, 63.239
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-130-

GOL

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Components

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


Mass: 13705.299 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 / Glycerol


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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). E54G ...THE SEQUENCE IS BASED REFERENCE 96 IN THE DATABASE TTHY_HUMAN (UNIPROTKB/SWISS-PROT P02766). E54G 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 200 mM 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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24735 / Rmerge(I) obs: 0.043 / Net I/σ(I): 52.3

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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: 1.7→31.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.267 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23842 1265 5.1 %RANDOM
Rwork0.19993 ---
obs0.2019 23436 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 28 164 1967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221855
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9562529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2823.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.459158
X-RAY DIFFRACTIONr_chiral_restr0.1610.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211398
X-RAY DIFFRACTIONr_mcbond_it1.2791.51157
X-RAY DIFFRACTIONr_mcangle_it2.26621876
X-RAY DIFFRACTIONr_scbond_it3.6013698
X-RAY DIFFRACTIONr_scangle_it5.734.5653
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 72 -
Rwork0.239 1352 -
obs--75.83 %
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)
10.84470.32340.15561.1156-0.15880.8708-0.0293-0.13930.03560.0213-0.10090.12540.0449-0.05230.1303-0.0375-0.01060.0255-0.0849-0.0147-0.0025-13.195-0.606-5.884
21.4162-0.36080.62690.8312-0.15250.6917-0.0120.1639-0.0605-0.1041-0.04390.1244-0.02210.02190.0560.00780.0025-0.0135-0.0947-0.0053-0.0055-12.672-3.034-25.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 125
2X-RAY DIFFRACTION2B10 - 124

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