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- PDB-3d7p: Crystal structure of human Transthyretin (TTR) at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 3d7p
TitleCrystal structure of human Transthyretin (TTR) at pH 4.0
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / wt-TTR / AMYLOID / TRANSTHYRETIN / ACIDIC PH / native TTR / and crystal structure / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hormone / Polymorphism / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPalaninathan, S.K. / Mohamedmohaideen, N.N. / Snee, W.C. / Kelly, J.W. / Sacchettini, J.C.
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
DepositionMay 21, 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 ...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
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
Water2,828157
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 area5840 Å2
ΔGint-36 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.224, 85.082, 62.920
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-135-

HOH

21A-179-

HOH

31B-144-

HOH

41B-165-

HOH

51B-176-

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.: 157 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: TTR pH 4.0 crystals were grown in the presence of 0.1 M sodium acetate (pH 4.0), 100 mM KCl, 1 mM EDTA and 0.3-0.5 M ammonium sulfate which was equilibrated against 2 M ammonium sulfate in ...Details: TTR pH 4.0 crystals were grown in the presence of 0.1 M sodium acetate (pH 4.0), 100 mM KCl, 1 mM EDTA and 0.3-0.5 M ammonium sulfate which was equilibrated against 2 M ammonium sulfate in hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jan 10, 2003 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.72→22.19 Å / Num. all: 25276 / Num. obs: 25276 / % possible obs: 99.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.72→1.76 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMZ

1bmz


Resolution: 1.72→22.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.613 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24943 1290 5.1 %RANDOM
Rwork0.22129 ---
all0.22276 25276 --
obs0.22276 25276 99.68 %-
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 mean: 24.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.72→22.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 0 157 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221799
X-RAY DIFFRACTIONr_bond_other_d0.0020.021165
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9392454
X-RAY DIFFRACTIONr_angle_other_deg0.85432849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0035228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.22423.61172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.869157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_nbd_refined0.1790.2272
X-RAY DIFFRACTIONr_nbd_other0.1940.21110
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2860
X-RAY DIFFRACTIONr_nbtor_other0.0840.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.28
X-RAY DIFFRACTIONr_mcbond_it1.0941.51456
X-RAY DIFFRACTIONr_mcbond_other0.1471.5465
X-RAY DIFFRACTIONr_mcangle_it1.19821845
X-RAY DIFFRACTIONr_scbond_it1.783787
X-RAY DIFFRACTIONr_scangle_it2.684.5609
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 86 -
Rwork0.276 1699 -
obs--97.12 %

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