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

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Basic information

Entry
Database: PDB / ID: 4pvm
TitleNeutron structure of human transthyretin (TTR) at room temperature to 2.0A resolution (Laue)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / BETA SANDWICH / SERUM
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
DEUTERATED WATER / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / Resolution: 2 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: Data collection / Refinement description / Category: diffrn_radiation / software / Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 2.0Mar 20, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)28,0732
Polymers28,0732
Non-polymers00
Water1,60389
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-220-

DOD

21A-221-

DOD

31A-221-

DOD

41A-247-

DOD

51B-215-

DOD

61B-235-

DOD

71B-237-

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.: 89 / 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: 2.21 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, 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 REACTOROTHER13.18-4.22
SYNCHROTRONESRF ID23-120.9791
Detector
TypeIDDetectorDate
LADI-III1IMAGE PLATEMay 12, 2010
ADSC QUANTUM 315r2CCDFeb 12, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NiTi multilayer filterLAUELneutron1
2SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
13.181
24.221
30.97911
Reflection

Entry-ID: 4PVM

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)Biso Wilson estimate (Å2)
2-43.68172161348078.3225.10.18217.3
1.85-43.132171899.423.50.09327.419.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2-2.1140.3373.41524162.1
1.85-1.953.490.422.67297.9

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Processing

Software
NameVersionClassification
QLDdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_914)refinement
LAUEGENdata reduction
LSCALEdata scaling
SCALAdata scaling
PHENIXphasing
Refinement

Baniso 12: -0 Å2 / % reflection Rfree: 10.01 % / Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBaniso 11 (Å2)Baniso 13 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% 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
2-36.378NEUTRON DIFFRACTION-1.0713-00.459300.6120.27090.20860.214713411339176.9311.4631.420.591
1.95-43.13X-RAY DIFFRACTION-0.30740-0.0845-00.3920.20250.15290.157718671865599.4421.3442.430.3986.4825.176.77167880.81820.1717.88
Refinement stepCycle: LAST / Resolution: 2→36.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 0 89 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0133836
NEUTRON DIFFRACTIONf_angle_d1.3546829
NEUTRON DIFFRACTIONf_chiral_restr0.082289
NEUTRON DIFFRACTIONf_plane_restr0.007669
NEUTRON DIFFRACTIONf_dihedral_angle_d17.9291029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.0001-2.07160.32011030.2797923NEUTRON DIFFRACTION10261060
2.0716-2.15450.32131100.2524987NEUTRON DIFFRACTION10971065
2.1545-2.25260.29421140.24311021NEUTRON DIFFRACTION11351066
2.2526-2.37130.25441120.25161014NEUTRON DIFFRACTION11261066
2.3713-2.51990.32481220.24741103NEUTRON DIFFRACTION12251072
2.5199-2.71440.30341400.24291254NEUTRON DIFFRACTION13941080
2.7144-2.98740.29621460.20251303NEUTRON DIFFRACTION14491084
2.9874-3.41940.23091540.19261396NEUTRON DIFFRACTION15501088
3.4194-4.3070.23441660.14871488NEUTRON DIFFRACTION16541094
4.307-36.3840.24161740.18141561NEUTRON DIFFRACTION17351093
1.95-2.00270.21951420.17281274X-RAY DIFFRACTION141613100
2.0027-2.06170.21631410.16471277X-RAY DIFFRACTION141813100
2.0617-2.12820.19751420.15241270X-RAY DIFFRACTION141213100
2.1282-2.20430.21631420.14621274X-RAY DIFFRACTION141613100
2.2043-2.29250.19381410.15291269X-RAY DIFFRACTION141013100
2.2925-2.39680.18571430.14471288X-RAY DIFFRACTION143113100
2.3968-2.52320.2161410.15081276X-RAY DIFFRACTION141713100
2.5232-2.68130.22191420.1581276X-RAY DIFFRACTION141813100
2.6813-2.88820.21191440.16351297X-RAY DIFFRACTION144113100
2.8882-3.17880.20661440.16021296X-RAY DIFFRACTION14401399
3.1788-3.63860.19971460.14711311X-RAY DIFFRACTION14571399
3.6386-4.58340.18661460.13081307X-RAY DIFFRACTION14531399
4.5834-43.14050.19951530.16591373X-RAY DIFFRACTION15261397

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