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- PDB-2try: TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS... -

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Basic information

Entry
Database: PDB / ID: 2try
TitleTERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND IMPLICATIONS FOR AMYLOID FIBRIL FORMATION
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT / ALBUMIN / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / THYROXINE / PREALBUMIN
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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 / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / 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: 2 Å
AuthorsSchormann, N. / Murrell, J.R. / Benson, M.D.
CitationJournal: Amyloid / Year: 1998
Title: Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation.
Authors: Schormann, N. / Murrell, J.R. / Benson, M.D.
History
DepositionOct 21, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)27,7072
Polymers27,7072
Non-polymers00
Water93752
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,4144
Polymers55,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6180 Å2
ΔGint-45 kcal/mol
Surface area21110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.670, 86.370, 64.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99044, 0.13681, -0.01781), (0.13664, 0.99057, -0.01035), (-0.01906, -0.00782, -0.99979)
Vector: 36.462, -1.931, 97.905)

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Components

#1: Protein TRANSTHYRETIN / PREALBUMIN


Mass: 13853.457 Da / Num. of mol.: 2 / Mutation: VARIANT S77Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HB101 / Plasmid: PCZ11 / Cell line (production host): HB101 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.2 Å3/Da / Density % sol: 52.5 %
Crystal growpH: 6.5
Details: PURIFIED PROTEIN (25MG/ML IN 100MM TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM 1.5M AMMONIUM SULFATE, 100MM CITRATE BUFFER, PH 5.5, AT ROOM TEMPERATURE., pH 6.5
PH range: 5.5-7.5 / Temp details: room temp

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→64.9 Å / Num. obs: 17581 / % possible obs: 74.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.091 / Net I/σ(I): 5
Reflection shellResolution: 1.8→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.22 / % possible all: 56

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
bioteXdata reduction
bioteXdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTA

1tta


Resolution: 2→5 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 515.8 / Data cutoff low absF: 7 / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES IN REGIONS WITH LOW ELECTRON DENSITY (RESIDUES 1 - 9 AT N-TERMINUS AND RESIDUES 124 - 127 AT C-TERMINUS) WERE REFINED WITH OCCUPANCIES SET TO 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.31 846 5 %RANDOM
Rwork0.213 ---
obs0.213 12667 79.1 %-
Displacement parametersBiso mean: 19.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 52 2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.221.5
X-RAY DIFFRACTIONx_mcangle_it1.412
X-RAY DIFFRACTIONx_scbond_it1.412
X-RAY DIFFRACTIONx_scangle_it1.582.5
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.365 58 4.6 %
Rwork0.31 1202 -
obs--63.83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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