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- PDB-1bzd: TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS... -

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Basic information

Entry
Database: PDB / ID: 1bzd
TitleTERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND IMPLICATIONS FOR AMYLOID FIBRIL FORMATION
ComponentsPROTEIN (TRANSTHYRETIN)
KeywordsBINDING PROTEIN / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / TRANSPORT / THYROXINE
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: 1.9 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 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)


Theoretical massNumber of molelcules
Total (without water)27,6152
Polymers27,6152
Non-polymers00
Water1,22568
1
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)

A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)


Theoretical massNumber of molelcules
Total (without water)55,2304
Polymers55,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6260 Å2
ΔGint-45 kcal/mol
Surface area20700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.400, 86.120, 65.480
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: (-0.99066, 0.12928, -0.04335), (0.13001, 0.99141, -0.01443), (0.04111, -0.01993, -0.99896)
Vector: 39.14445, -1.93654, 97.61119)

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Components

#1: Protein PROTEIN (TRANSTHYRETIN) / PREALBUMIN


Mass: 13807.388 Da / Num. of mol.: 2 / Mutation: G6S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: VARIANT WAS PRODUCED BY SITE DIRECTED MUTAGENESIS USING THE NORMAL R-TTR-PCZ11 CONSTRUCT
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.: 68 / 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: 56.1 %
Crystal growpH: 5.5
Details: PURIFIED PROTEIN (20MG/ML IN 25MM MONOBASIC SODIUM PHOSPHATE BUFFER, 0.15M NACL) WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 100MM CITRATE BUFFER, PH 5.5 AT ROOM TEMPERATURE.
Temp details: room temp
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
225 mMmonobasic sodium phosphate1drop
30.15 M1dropNaCl
41.5-3 Mammonium sulfate1reservoir
5100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→52.1 Å / Num. obs: 19822 / % possible obs: 67.8 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.075 / Rsym value: 0.039 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.22 / % possible all: 49
Reflection
*PLUS
Num. measured all: 146964

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Processing

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

1tsh


Resolution: 1.9→6 Å / Isotropic thermal model: RESTRAINED / 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
Rfree0.265 958 5 %RANDOM
Rwork0.188 ---
obs0.188 14612 75.8 %-
Displacement parametersBiso mean: 28 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 68 2016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.81
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_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 58 4.4 %
Rwork0.3 1320 -
obs--58.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.3

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