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- PDB-4pvl: X-ray structure of human transthyretin (TTR) at room temperature ... -

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Basic information

Entry
Database: PDB / ID: 4pvl
TitleX-ray structure of human transthyretin (TTR) at room temperature to 1.9A resolution
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / BETA SANDWICH / SERUM
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 / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsFisher, S.J. / Blakeley, M.P. / Haupt, M. / Mason, S.A. / Cooper, J.B. / Mitchell, E.P. / Forsyth, V.T.
CitationJournal: IUCrJ / Year: 2014
Title: Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein
Authors: Haupt, M. / Blakeley, M.P. / Fisher, S.J. / Mason, S.A. / Cooper, J.B. / Mitchell, E.P. / Forsyth, V.T.
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 8, 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: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)28,0732
Polymers28,0732
Non-polymers00
Water2,666148
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)56,1474
Polymers56,1474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6160 Å2
ΔGint-47 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.680, 86.260, 65.720
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-215-

HOH

21A-225-

HOH

31B-210-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 14036.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: PETM-11 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.15M SODIUM MALONATE, 23MG/ML PROTEIN, 100UL DROP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→43.13 Å / Num. obs: 21718 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21.69 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.67 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE: 1.7.3_914)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IPE

3ipe


Resolution: 1.851→43.13 Å / FOM work R set: 0.8831 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 2169 10.01 %
Rwork0.1516 19507 -
obs0.1563 21676 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.52 Å2 / Biso mean: 27.92 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: LAST / Resolution: 1.851→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 148 1940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111866
X-RAY DIFFRACTIONf_angle_d1.2822552
X-RAY DIFFRACTIONf_chiral_restr0.076290
X-RAY DIFFRACTIONf_plane_restr0.008327
X-RAY DIFFRACTIONf_dihedral_angle_d14.428664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.851-1.89410.35011370.271239137695
1.8941-1.94150.2341420.198212661408100
1.9415-1.9940.19761430.174812921435100
1.994-2.05260.19911440.162412941438100
2.0526-2.11890.19561410.15612811422100
2.1189-2.19460.21911450.14513011446100
2.1946-2.28250.2011440.143312801424100
2.2825-2.38630.17681420.136612871429100
2.3863-2.51210.21721430.153712911434100
2.5121-2.66950.21011470.153113171464100
2.6695-2.87560.21531450.161913101455100
2.8756-3.16490.21491460.16221311145799
3.1649-3.62270.20431460.13731321146799
3.6227-4.56340.1691480.12181326147499
4.5634-43.14170.17891560.15381391154797

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