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- PDB-4iki: Crystal structure of wild-type human transthyretin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4iki
TitleCrystal structure of wild-type human transthyretin in complex with indomethacin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone carrier / Retinol binding protein
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
INDOMETHACIN / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLima, L.M.T.R. / Polikarpov, I.
CitationJournal: To be Published
Title: Crystal structure of wild-type human transthyretin in complex with indomethacin
Authors: Lima, L.M.T.R. / Polikarpov, I.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)28,2704
Polymers27,5552
Non-polymers7162
Water2,288127
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5418
Polymers55,1094
Non-polymers1,4314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9350 Å2
ΔGint-68 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.090, 86.120, 63.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-201-

IMN

21B-329-

HOH

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Components

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


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-IMN / INDOMETHACIN / Indometacin


Mass: 357.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10mg/mL wtTTR, 22% peg 400, 100mM Tris pH 7.4, 100mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→63.52 Å / Num. all: 16478 / Num. obs: 16478 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.116.40.4460.411.81479023280.1710.4460.414.398.9
2.11-2.246.40.2940.272.81422422220.1130.2940.276.698.9
2.24-2.396.40.2370.2183.41335820970.0910.2370.2188.998.9
2.39-2.586.40.170.1574.81244819400.0660.170.15712.299.1
2.58-2.836.40.1180.1096.81189118450.0460.1180.10916.999.8
2.83-3.166.70.0790.0739.81117716610.030.0790.07324.5100
3.16-3.656.90.0490.045151019014860.0180.0490.04536.2100
3.65-4.476.80.0390.03616.7872612740.0150.0390.03646.7100
4.47-6.326.70.0310.02918.8685210210.0120.0310.02953.7100
6.32-43.0736.10.0330.031336796040.0140.0330.0348.199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.26 Å43.06 Å
Translation2.26 Å43.06 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.2.25data reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2199 / WRfactor Rwork: 0.1619 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8674 / SU B: 3.888 / SU ML: 0.109 / SU R Cruickshank DPI: 0.194 / SU Rfree: 0.1779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 830 5 %RANDOM
Rwork0.1716 ---
obs0.1746 16452 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.9 Å2 / Biso mean: 24.922 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2---0.99 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 50 127 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192100
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.972902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1224.36294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91615319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6021510
X-RAY DIFFRACTIONr_chiral_restr0.1420.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211704
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 67 -
Rwork0.213 1130 -
all-1197 -
obs--97.87 %

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