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- PDB-4pvn: Neutron structure of human transthyretin (TTR) at room temperatur... -

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Basic information

Entry
Database: PDB / ID: 4pvn
TitleNeutron structure of human transthyretin (TTR) at room temperature to 2.3A resolution (monochromatic)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / BETA SANDWICH / SERUM
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
DEUTERATED WATER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Water1,51384
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
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-216-

DOD

21A-223-

DOD

31A-235-

DOD

41B-217-

DOD

51B-217-

DOD

61B-227-

DOD

71B-229-

DOD

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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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2.15M SODIUM MALONATE, 23MG/ML PROTEIN, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTOROTHER12.42
SYNCHROTRONESRF ID23-120.9791
Detector
TypeIDDetectorDate
HE3 POSITION SENSITIVE DETECTOR1AREA DETECTORJun 23, 2010
ADSC QUANTUM 315r2CCDFeb 12, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Graphite (002)SINGLE WAVELENGTHMneutron1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.421
20.97911
Reflection

Entry-ID: 4PVN

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.3-52.276114381139599.31.31.33.514.90.15217.7
1.85-43.132171899.423.519.80.09327.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.422.60.6451.61613198.7
1.85-1.953.490.422.67297.9

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Processing

Software
NameVersionClassification
MADSYSphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_914)refinement
RETREATdata reduction
SCALAdata scaling
PHENIXphasing
Refinement

Baniso 13: 0 Å2 / Baniso 23: -0 Å2 / Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureResolution (Å)Refine-IDBaniso 11 (Å2)Baniso 12 (Å2)Baniso 22 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Bsol (Å2)ksol (e/Å3)Biso max (Å2)Biso mean (Å2)Biso min (Å2)Num. reflection RworkFOM work R setSU MLPhase error
2.3-52.276NEUTRON DIFFRACTION-1.80402.1028-0.29880.2620.20930.2118571113955.0198.6211.3527.2890.6
MOLECULAR REPLACEMENT1.95-43.13X-RAY DIFFRACTION-0.2524-0-0.10380.35620.18510.1560.157493318655599.4421.3434.7120.39197.6429.5611.15177220.82150.1817.27
Refinement stepCycle: LAST / Resolution: 2.3→52.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 0 84 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0123800
NEUTRON DIFFRACTIONf_angle_d1.3096774
NEUTRON DIFFRACTIONf_chiral_restr0.084289
NEUTRON DIFFRACTIONf_plane_restr0.007644
NEUTRON DIFFRACTIONf_dihedral_angle_d15.6271029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.3001-2.53150.32181390.25822630NEUTRON DIFFRACTION2769498
2.5315-2.89780.31331400.23932660NEUTRON DIFFRACTION2800499
2.8978-3.65080.24661440.19952734NEUTRON DIFFRACTION28784100
3.6508-52.28980.22081480.17982800NEUTRON DIFFRACTION2948498
1.95-2.05280.22591290.18532512X-RAY DIFFRACTION26417100
2.0528-2.18140.21021340.15552482X-RAY DIFFRACTION26167100
2.1814-2.34980.17941300.1492499X-RAY DIFFRACTION26297100
2.3498-2.58630.19391330.15422507X-RAY DIFFRACTION26407100
2.5863-2.96050.18651340.15912530X-RAY DIFFRACTION26647100
2.9605-3.72950.17331330.15072554X-RAY DIFFRACTION2687799
3.7295-43.14050.17611400.15472638X-RAY DIFFRACTION2778798

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