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- PDB-3cft: Crystal structure of human transthyretin in complex with 1-amino-... -

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Basic information

Entry
Database: PDB / ID: 3cft
TitleCrystal structure of human transthyretin in complex with 1-amino-5-naphthalene sulfonate
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human wild-type transthyretin / thyroxin / amyloid / familial amyloid polyneurophaty / Disease mutation / Glycoprotein / Hormone / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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
5-aminonaphthalene-1-sulfonic acid / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsLima, L.-M.T.R. / Foguel, D. / Polikarpov, I.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Identification of a novel ligand binding motif in the transthyretin channel.
Authors: Lima, L.M. / Silva, V.D. / Palmieri, L.D. / Oliveira, M.C. / Foguel, D. / Polikarpov, I.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)26,5935
Polymers25,9232
Non-polymers6703
Water2,540141
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,18610
Polymers51,8464
Non-polymers1,3396
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6260 Å2
ΔGint-45.4 kcal/mol
Surface area18950 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-10.5 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.960, 85.610, 63.800
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-1-

5NS

21B-1-

5NS

31B-1-

5NS

41B-128-

5NS

51B-128-

5NS

61A-151-

HOH

71B-137-

HOH

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Components

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


Mass: 12961.511 Da / Num. of mol.: 2 / Fragment: UNP residues 30-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-5NS / 5-aminonaphthalene-1-sulfonic acid


Mass: 223.248 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9NO3S
#3: Water ChemComp-HOH / water / 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: 2.26 Å3/Da / Density % sol: 45.64 %

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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: Jun 2, 2005 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→85.749 Å / Num. all: 20234 / Num. obs: 19759 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.87-1.9640.4571.6978824230.45783.1
1.96-2.084.10.3182.41109926920.31898
2.08-2.224.10.18941054825610.18998.4
2.22-2.44.10.1544.8989924210.15499
2.4-2.634.20.1056.9932722380.10599.6
2.63-2.944.20.06411.4861720460.06499.7
2.94-3.44.20.04216.1768418290.042100
3.4-4.164.20.03417.2654015610.034100
4.16-5.884.10.02419.3516012520.024100
5.88-42.963.80.02516.827867360.02599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.06 Å42.81 Å
Translation2.06 Å42.81 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CFM

3cfm


Resolution: 1.87→38.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.763 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1017 5.1 %RANDOM
Rwork0.191 ---
all0.194 20234 --
obs0.194 19755 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.87→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 45 141 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222042
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9682810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83723.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26215319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.345159
X-RAY DIFFRACTIONr_chiral_restr0.1850.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021599
X-RAY DIFFRACTIONr_nbd_refined0.2150.2853
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.226
X-RAY DIFFRACTIONr_mcbond_it1.2291.51279
X-RAY DIFFRACTIONr_mcangle_it1.96322045
X-RAY DIFFRACTIONr_scbond_it2.9483916
X-RAY DIFFRACTIONr_scangle_it4.5564.5765
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 56 -
Rwork0.298 1282 -
all-1338 -
obs--92.72 %

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