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- PDB-4ik6: Crystal structure of human transthyretin in complex with lumiracoxib -

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Basic information

Entry
Database: PDB / ID: 4ik6
TitleCrystal structure of human transthyretin in complex with lumiracoxib
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / hormone carrier / retinol binding protein
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / : / protein-containing complex / 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
Chem-LUR / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLima, L.M.T.R.
CitationJournal: To be Published
Title: Crystal structure of human transthyretin in complex with lumiracoxib
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)28,1424
Polymers27,5552
Non-polymers5872
Water2,252125
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2848
Polymers55,1094
Non-polymers1,1754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6190 Å2
ΔGint-42 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.860, 83.220, 62.850
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-201-

LUR

21A-201-

LUR

31B-201-

LUR

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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-LUR / {2-[(2-chloro-6-fluorophenyl)amino]-5-methylphenyl}acetic acid / Lumiracoxib


Mass: 293.721 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClFNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
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: MAR CCD 165 mm / 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→83.333 Å / Num. all: 15410 / Num. obs: 15410 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 18.7
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
2-2.113.30.390.3282.1726222000.210.390.3283.199.9
2.11-2.243.30.3170.2672.6693320980.170.3170.267599.9
2.24-2.393.30.2120.1783.9649019690.1140.2120.1786.499.8
2.39-2.583.30.1390.1166.2607918290.0740.1390.1169.699.9
2.58-2.833.30.1020.0868572217110.0550.1020.08614.4100
2.83-3.163.40.0710.0611.2524815550.0380.0710.0622.7100
3.16-3.653.40.0460.03916471913840.0240.0460.03937.4100
3.65-4.473.30.0550.04611.7395911910.030.0550.04646.1100
4.47-6.323.30.0390.03315.530949430.0210.0390.03352100
6.32-21.7033.10.0330.02720.516215300.0180.0330.02748.795.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.18 Å21.7 Å
Translation2.18 Å21.7 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2144 / WRfactor Rwork: 0.1743 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8333 / SU B: 4.81 / SU ML: 0.136 / SU R Cruickshank DPI: 0.2514 / SU Rfree: 0.1913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 766 5 %RANDOM
Rwork0.1923 ---
obs0.1946 15377 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 89.81 Å2 / Biso mean: 32.0996 Å2 / Biso min: 15.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-0 Å2
2---1.57 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→21.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 40 125 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192240
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9553105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13723.64696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.815351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3591510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211835
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 47 -
Rwork0.232 1055 -
all-1102 -
obs--99.91 %

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