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- PDB-1bmz: HUMAN TRANSTHYRETIN (PREALBUMIN) -

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Basic information

Entry
Database: PDB / ID: 1bmz
TitleHUMAN TRANSTHYRETIN (PREALBUMIN)
ComponentsPROTEIN (TRANSTHYRETIN)
KeywordsHORMONE/GROWTH FACTOR / THYROXINE TRANSPORT / HORMONE-GROWTH FACTOR COMPLEX
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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 / OTHER / Resolution: 2 Å
AuthorsKlabunde, T. / Kelly, J.W. / Sacchettini, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Inhibiting transthyretin conformational changes that lead to amyloid fibril formation.
Authors: Peterson, S.A. / Klabunde, T. / Lashuel, H.A. / Purkey, H. / Sacchettini, J.C. / Kelly, J.W.
History
DepositionJul 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)


Theoretical massNumber of molelcules
Total (without water)27,5552
Polymers27,5552
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area10100 Å2
MethodPISA
2
A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (TRANSTHYRETIN)

A: PROTEIN (TRANSTHYRETIN)
B: PROTEIN (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_665-x+1,-y+1,z1
Buried area6080 Å2
ΔGint-49 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.850, 85.800, 64.800
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: (-0.985414, 0.170065, 0.006154), (0.169995, 0.985389, -0.010495), (-0.007849, -0.009296, -0.999926)
Vector: 35.0238, -2.8161, 32.6005)

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Components

#1: Protein 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) / Organ: PLASMA / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mM1dropKCl
3100 mMphosphate1drop
41 Mammonium sulfate1drop
52 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16218 / % possible obs: 96.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.052 / Rsym value: 5.2 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.117 / Rsym value: 11.7 / % possible all: 84
Reflection
*PLUS
Num. measured all: 64327
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→6 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1462 10 %RANDOM
Rwork0.183 ---
obs0.183 14732 91.7 %-
Displacement parametersBiso mean: 29.6 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 0 52 1814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.013
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.1218 Å / Weight position: 100
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20 /
Rfactor% reflection
Rfree0.3 10 %
Rwork0.222 -
obs-70.8 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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