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- PDB-1bz8: TRANSTHYRETIN (DEL VAL122) -

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Basic information

Entry
Database: PDB / ID: 1bz8
TitleTRANSTHYRETIN (DEL VAL122)
ComponentsPROTEIN (TRANSTHYRETIN)
KeywordsSIGNALING PROTEIN / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / DELETION MUTANT / TRANSPORT / THYROXINE
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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. / Uemichi, T. / Benson, M.D.
CitationJournal: To be Published
Title: Structural Analysis of Delval122 Transthyretin-A Deletion Mutant
Authors: Schormann, N. / Uemichi, T. / Benson, M.D.
History
DepositionNov 8, 1998Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Aug 9, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)27,3562
Polymers27,3562
Non-polymers00
Water70339
1
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)

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


Theoretical massNumber of molelcules
Total (without water)54,7134
Polymers54,7134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6220 Å2
ΔGint-39 kcal/mol
Surface area20520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.330, 86.750, 65.050
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: (-0.9919, 0.12697, -0.00413), (0.127, 0.99188, -0.00622), (0.0033, -0.0067, -0.99997)
Vector: 31.67888, -2.30646, 97.70567)

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Components

#1: Protein PROTEIN (TRANSTHYRETIN) / PREALBUMIN


Mass: 13678.229 Da / Num. of mol.: 2 / Mutation: TRINUCLEOTIDE DELETION VARIANT DELVAL122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: VARIANT WAS PRODUCED BY SITE DIRECTED MUTAGENESIS USING A MISMATCH PRIMER AND 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.: 39 / 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: 2.3 Å3/Da / Density % sol: 44.92 %
Description: AFTER INITIAL REFINEMENT THE C-TERMINAL RESIDUES WERE REBUILT USING AN OMIT MAP, SINCE THE DELETION RESULTS IN A REMOVAL OF VALINE AT POSITION 122
Crystal growpH: 6.5 / Details: pH 6.50

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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 1, 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: 1.8→65.1 Å / Num. obs: 17380 / % possible obs: 74 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.052 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.22 / % possible all: 56.5

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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: 2→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 122 - 126 AT C-TERMINUS) WERE REFINED WITH OCCUPANCIES SET TO 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 835 5 %RANDOM
Rwork0.193 ---
obs0.193 13478 81.1 %-
Displacement parametersBiso mean: 28.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 0 39 1969
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_deg2.01
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_d1.51
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: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 75 6.1 %
Rwork0.29 1231 -
obs--64.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP

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