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

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Basic information

Entry
Database: PDB / ID: 4iiz
TitleCrystal structure of wild-type human transthyretin in complex with lumiracoxib
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloid / RBP carrier
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: 2.1 Å
AuthorsLima, L.M.T.R.
CitationJournal: To be Published
Title: Crystal structure of wild-type human transthyretin in complex with lumiracoxib
Authors: Lima, L.M.T.R.
History
DepositionDec 20, 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

Downloads & links

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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
Water1,946108
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 area6080 Å2
ΔGint-44 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 83.000, 62.950
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

31A-201-

LUR

41B-201-

LUR

51B-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.: 108 / 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: 38.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / 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→83.045 Å / Num. all: 13337 / Num. obs: 13337 / % possible obs: 99.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 20.6
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
2.1-2.213.20.3110.262.7600819060.1660.3110.264100
2.21-2.353.20.2570.2173.4578418020.1350.2570.2174.999.9
2.35-2.513.20.1840.1554.7555917190.0960.1840.1557.1100
2.51-2.713.20.1370.1156.1512315840.0730.1370.11510.2100
2.71-2.973.20.0920.0779477514840.0490.0920.07716.699.9
2.97-3.323.20.0620.05211.9435413470.0330.0620.0522799.8
3.32-3.833.20.0420.03518.2384411920.0220.0420.03541.4100
3.83-4.73.20.0420.03516327510340.0220.0420.03553.199.9
4.7-6.643.10.0390.03215.925268100.0210.0390.03250.999.8
6.64-21.6732.90.0410.03314.713374590.0240.0410.03352.195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.45 Å21.67 Å
Translation2.45 Å21.67 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: 2.1→21.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2096 / WRfactor Rwork: 0.1529 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8273 / SU B: 5.443 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2864 / SU Rfree: 0.2154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 658 4.9 %RANDOM
Rwork0.1725 ---
obs0.1755 13312 99.62 %-
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: 99.58 Å2 / Biso mean: 31.193 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-0 Å2
2---1.6 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 40 108 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192217
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.9563072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1845296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05723.68495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46815346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8511510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211812
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 44 -
Rwork0.16 908 -
all-952 -
obs--99.9 %

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