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- PDB-1iii: CRYSTAL STRUCTURE OF THE TRANSTHYRETIN MUTANT TTR Y114C-DATA COLL... -

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Basic information

Entry
Database: PDB / ID: 1iii
TitleCRYSTAL STRUCTURE OF THE TRANSTHYRETIN MUTANT TTR Y114C-DATA COLLECTED AT ROOM TEMPERATURE
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / GREEK KEY / BETA BARREL
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
BETA-MERCAPTOETHANOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsEneqvist, T. / Olofsson, A. / Ando, Y. / Lundgren, E. / Sauer-Eriksson, A.E.
CitationJournal: Biochemistry / Year: 2002
Title: Disulfide-Bond Formation in the Transthyretin Mutant Y114C Prevents Amyloid Fibril Formation in Vivo and in Vitro
Authors: Eneqvist, T. / Olofsson, A. / Ando, Y. / Miyakawa, T. / Katsuragi, S. / Jass, J. / Lundgren, E. / Sauer-Eriksson, A.E.
History
DepositionApr 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9038
Polymers27,4352
Non-polymers4696
Water2,540141
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules

A: TRANSTHYRETIN
B: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,80716
Polymers54,8694
Non-polymers93812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7190 Å2
ΔGint-50 kcal/mol
Surface area20120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.517, 86.140, 65.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-977-

HOH

21B-933-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, -y, z.

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Components

#1: Protein TRANSTHYRETIN / TBPA / TTR / ATTR


Mass: 13717.329 Da / Num. of mol.: 2 / Fragment: TRANSTHYRETIN / Mutation: Y114C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR / Plasmid: PET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2M ammonium sulphate, 0.1M sodium citrate, 2% PEG 200, 1% BME, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
250 mMTris1droppH7.5
32 Mammonium sulfate1reservoir
4100 mMsodium citrate1reservoir
52 %PEG2001reservoir
61 %beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 3, 1998
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17049 / Num. obs: 17049 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1661 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 155823
Reflection shell
*PLUS
% possible obs: 97.2 % / Num. unique obs: 1661

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1F41

1f41


Resolution: 2→19.54 Å / SU B: 5.509 / SU ML: 0.1578 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2109 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber
Details: Occupancy of BME molecules were refined after structural overall B-factor refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1721 11.2 %RANDOM
Rwork0.1971 ---
all0.201 15298 --
obs0.201 15298 100 %-
Displacement parametersBiso mean: 19.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 24 141 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.021
X-RAY DIFFRACTIONp_angle_d1.2121.937
X-RAY DIFFRACTIONp_mcbond_it0.7311.5
X-RAY DIFFRACTIONp_mcangle_it1.4192
X-RAY DIFFRACTIONp_scbond_it1.9263
X-RAY DIFFRACTIONp_scangle_it3.3734.5
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.0740.2
X-RAY DIFFRACTIONp_singtor_nbd3.53
X-RAY DIFFRACTIONp_multtor_nbd16.82115
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2010.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1680.5
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 19.5 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.211.937

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