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- PDB-1u21: transthyretin with tethered inhibitor on one monomer. -

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Basic information

Entry
Database: PDB / ID: 1u21
Titletransthyretin with tethered inhibitor on one monomer.
ComponentsTransthyretin
KeywordsHORMONE/GROWTH FACTOR / transthyretin / amyloid / HORMONE-GROWTH FACTOR COMPLEX
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
Chem-P2C / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWiseman, R.L. / Johnson, S.M. / Kelker, M.S. / Foss, T. / Wilson, I.A. / Kelly, J.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Kinetic stabilization of an oligomeric protein by a single ligand binding event
Authors: Wiseman, R.L. / Johnson, S.M. / Kelker, M.S. / Foss, T. / Wilson, I.A. / Kelly, J.W.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 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
Remark 999 SEQUENCE Three of the four monomers in the transthyretin tetramer contained a C10A mutation. The ... SEQUENCE Three of the four monomers in the transthyretin tetramer contained a C10A mutation. The fourth monomer was wildtype, with a Cys at the 10 position and was chemically linked via a disulfide bridge to the P2C small molecule. However due to crystal symmetry and the statistically random way in which the tetramers were added to the crystal, there is no way tO distinguish the subunits apart. Therefore each chain in the asymmetric unit contains the wild type sequence. The C10A mutant monomer has DYKDDDYKDYKDDDYK added to the N-terminus and the vector used was the plamid PMMHa. See the paper for details.

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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)28,2154
Polymers27,5552
Non-polymers6602
Water1,874104
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4308
Polymers55,1094
Non-polymers1,3204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area8900 Å2
ΔGint-100 kcal/mol
Surface area18480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.654, 85.643, 63.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-211-

P2C

21A-211-

P2C

DetailsThe biological assembly is a teteramer generated from the dimer in the asymmetric unit by the operation: 1 0 0 0 0 1 0 0 0 0 1 0 -1 0 0 43.65 0 -1 0 86.63 0 0 1 0

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Components

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


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: see remark 999 for mutation information / Source: (gene. exp.) Homo sapiens (human) / Gene: TTR; PALB; / Plasmid: pET2c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Epicurian Gold / References: UniProt: P02766
#2: Chemical ChemComp-P2C / 2-[(3,5-DICHLORO-4-TRIOXIDANYLPHENYL)AMINO]BENZOIC ACID / 2-[3,5-DICHLORO-4-(2-{2-[2(2-MERCAPTOETHOXY)ETHOXY]ETHOXY}ETHOXY)PHENYLAMINO]BENZOIC ACID


Mass: 330.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9Cl2NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, calcium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2004 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.69→27.63 Å / Num. all: 27493 / Num. obs: 26531 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.06 / Net I/σ(I): 33.2
Reflection shellResolution: 1.69→1.76 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2795 / Rsym value: 0.607 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BZD

1bzd


Resolution: 1.69→27.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.602 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SEE REMARK 999 FOR MUTATIONS AND FURTHER REFINEMENT INFORMATION
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 1283 4.8 %RANDOM
Rwork0.21676 ---
obs0.21783 25202 96.04 %-
all-27493 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.69→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 42 104 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211886
X-RAY DIFFRACTIONr_bond_other_d0.0020.021644
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9632574
X-RAY DIFFRACTIONr_angle_other_deg0.75933824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755230
X-RAY DIFFRACTIONr_chiral_restr0.0860.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022104
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02392
X-RAY DIFFRACTIONr_nbd_refined0.2120.3298
X-RAY DIFFRACTIONr_nbd_other0.2760.31835
X-RAY DIFFRACTIONr_nbtor_other0.0940.51167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.330
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.395
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.523
X-RAY DIFFRACTIONr_mcbond_it0.8951.51160
X-RAY DIFFRACTIONr_mcangle_it1.68121882
X-RAY DIFFRACTIONr_scbond_it2.6283726
X-RAY DIFFRACTIONr_scangle_it4.1944.5692
LS refinement shellResolution: 1.689→1.733 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.363 87
Rwork0.337 1534
obs-1534
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20391.4030.76252.09741.25241.4649-0.06160.1417-0.1437-0.08-0.01940.05330.0378-0.03480.0810.00370.00860.01450.1152-0.0150.082522.46229.84837.996
22.5525-1.37920.7882.7102-0.93731.8909-0.0134-0.1537-0.19920.2776-0.0657-0.06970.13140.08060.07910.0767-0.02610.01780.13060.02470.080919.99730.15757.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 12510 - 125
2X-RAY DIFFRACTION2BB10 - 12510 - 125

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