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- PDB-3cbr: Crystal structure of human Transthyretin (TTR) at pH3.5 -

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Basic information

Entry
Database: PDB / ID: 3cbr
TitleCrystal structure of human Transthyretin (TTR) at pH3.5
ComponentsTransthyretin
KeywordsTHYROXINE BINDING PROTEIN / TTR / AMYLOID / TRANSTHYRETIN / acidic pH / Disease mutation / Glycoprotein / Hormone / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Vitamin A / TRANSPORT 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMohamedmohaideen, N.N. / Palaninathan, S.K. / Snee, W.C. / Kelly, J.W. / C Sacchettini, J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural insight into pH-induced conformational changes within the native human transthyretin tetramer.
Authors: Palaninathan, S.K. / Mohamedmohaideen, N.N. / Snee, W.C. / Kelly, J.W. / Sacchettini, J.C.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,5552
Polymers27,5552
Non-polymers00
Water4,576254
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,1094
Polymers55,1094
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area6050 Å2
ΔGint-38.5 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.124, 85.494, 62.419
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-129-

HOH

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: PHNTR, PKNTR / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 5-7 mg/ml protein, 0.1 M sodium acetate, 20 % PEG 3350, 0.3-0.5 M ammonium sulfate equilibrated against 2.0M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2003
RadiationMonochromator: BENT GE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.91
ReflectionResolution: 1.63→35.58 Å / Num. all: 29348 / Num. obs: 29348 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 / Net I/σ(I): 19.36
Reflection shellResolution: 1.63→1.65 Å / Mean I/σ(I) obs: 2.69 / Rsym value: 0.69 / % possible all: 88.6

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Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMZ

1bmz


Resolution: 1.7→35.58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.277 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26048 1314 5.1 %RANDOM
Rwork0.22284 ---
all0.22472 24412 --
obs0.22472 24412 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.883 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 0 254 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221647
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9352242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.84623.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81115246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.807156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021222
X-RAY DIFFRACTIONr_nbd_refined0.1850.2707
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.221
X-RAY DIFFRACTIONr_mcbond_it0.7491.51065
X-RAY DIFFRACTIONr_mcangle_it1.25121687
X-RAY DIFFRACTIONr_scbond_it1.7383658
X-RAY DIFFRACTIONr_scangle_it2.9144.5555
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 110 -
Rwork0.268 1804 -
obs--100 %

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