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- PDB-4ik7: Crystal structure of human transthyretin in complex with indomethacin -

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Basic information

Entry
Database: PDB / ID: 4ik7
TitleCrystal structure of human transthyretin in complex with indomethacin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone carrier / RBP carrier / Retinol binding protein
Function / homology
Function and homology information


Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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 / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / 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
INDOMETHACIN / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLima, L.M.T.R.
CitationJournal: To be Published
Title: Crystal structure of human transthyretin in complex with indomethacin
Authors: Lima, L.M.T.R.
History
DepositionDec 25, 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 / 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

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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
Water2,558142
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 area9050 Å2
ΔGint-61 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.030, 83.570, 63.060
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
11A-376-

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.: 142 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Calcium chloride, 0.1M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.1→83.624 Å / Num. all: 13519 / Num. obs: 13519 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 12
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
2.1-2.213.40.4480.3771.9647619180.2380.4480.377399.9
2.21-2.353.40.4170.3522.1626018380.220.4170.3523.5100
2.35-2.513.40.3290.2762.2589117280.1770.3290.2765.1100
2.51-2.713.40.260.2183.1543516030.1390.260.2187100
2.71-2.973.40.1730.1430.9516715030.0960.1730.14310.4100
2.97-3.323.40.1010.0858.2464813610.0530.1010.08515.5100
3.32-3.833.40.0620.05212.8414712200.0330.0620.05223.1100
3.83-4.73.40.0550.04613352610440.0290.0550.04628.7100
4.7-6.643.30.040.0332027088190.0210.040.03327.7100
6.64-21.79130.0390.03217.314704850.0210.0390.0322797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.866 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 667 4.9 %RANDOM
Rwork0.2019 ---
obs0.2039 13517 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.97 Å2 / Biso mean: 27.7372 Å2 / Biso min: 11.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 50 142 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222014
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9752768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8635255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03423.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8815311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.951510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021590
X-RAY DIFFRACTIONr_nbd_refined0.2190.21065
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.220
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 45 -
Rwork0.244 901 -
all-946 -
obs--99.79 %

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