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- PDB-5dej: Transthyretin natural mutant A19D -

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Basic information

Entry
Database: PDB / ID: 5dej
TitleTransthyretin natural mutant A19D
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / TRANSTHYRETIN / IMMUNOGLOBULIN-LIKE / EXTRACELLULAR / HORMONE-BINDING PROTEIN
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, 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsPereira, H.M. / Ferreira, P. / Andrade, C. / Lima, C. / Palhano, F. / Foguel, D.
CitationJournal: To Be Published
Title: Crystal structure of human Transthyretin natural mutant A19D
Authors: Ferreira, P. / Pereira, H.M. / Andrade, C. / Lima, C. / Palhano, F. / Foguel, D.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_poly_seq_scheme / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _diffrn_source.pdbx_synchrotron_site / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5353
Polymers25,4942
Non-polymers401
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-18 kcal/mol
Surface area10880 Å2
MethodPISA
2
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0696
Polymers50,9894
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6500 Å2
ΔGint-58 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.930, 41.750, 62.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12747.227 Da / Num. of mol.: 2 / Fragment: UNP residues 30-145 / Mutation: A19D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02766
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 44.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES, 200 mM CaCl2 and 28% PEG400, pH 7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.37→41.75 Å / Num. all: 46599 / Num. obs: 46599 / % possible obs: 97.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.37-1.4140.5911098
6.13-41.753.80.0431093.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→37.552 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 2263 4.86 %
Rwork0.1785 44288 -
obs0.1799 46551 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.23 Å2 / Biso mean: 21.9055 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 1.37→37.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 0 232 1983
Biso mean---34.76 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071819
X-RAY DIFFRACTIONf_angle_d1.0732495
X-RAY DIFFRACTIONf_chiral_restr0.07290
X-RAY DIFFRACTIONf_plane_restr0.006316
X-RAY DIFFRACTIONf_dihedral_angle_d11.001631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.39980.3141430.27782747289098
1.3998-1.43240.27531640.25692729289397
1.4324-1.46820.25031420.23972748289097
1.4682-1.50790.25191360.22262630276693
1.5079-1.55230.21731560.20832773292998
1.5523-1.60240.21331340.20022800293498
1.6024-1.65960.21911670.20132760292798
1.6596-1.72610.28541130.19372822293599
1.7261-1.80460.24731440.19372841298598
1.8046-1.89980.21511460.1812784293098
1.8998-2.01880.19721430.16812744288797
2.0188-2.17470.17411170.16822660277792
2.1747-2.39350.18331360.17382795293197
2.3935-2.73970.21491390.17672827296697
2.7397-3.45140.20351340.17172835296996
3.4514-37.56640.18991490.15762793294291
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2825-0.49672.71594.646-4.32295.57340.21970.41840.2374-0.7558-0.3996-0.23960.30480.33870.12880.1680.0262-0.00570.1809-0.00520.121-7.9328-0.2983-29.9346
23.9355-1.94850.29422.1426-0.4620.9078-0.03790.0312-0.11510.02140.04240.1852-0.016-0.0634-0.01010.1324-0.008-0.0160.1499-0.01220.1455-17.5348-0.9583-25.5221
32.6681-4.31391.26468.3353-3.96265.13080.27760.6384-0.0565-0.6665-0.4553-0.09790.19010.12610.22450.16760.00880.00320.2342-0.01350.1716-9.6421-4.3851-34.2165
41.3768-1.49430.83672.6247-1.36112.2660.16270.2498-0.1255-0.2506-0.12620.38680.0891-0.0862-0.03490.120.0294-0.05250.1669-0.02030.1224-18.69827.199-28.9962
54.46264.4742-0.17426.3319-2.57273.3478-0.1760.1146-0.3333-0.15790.09970.00190.36810.03450.04730.1720.00180.03540.1263-0.02840.2274-12.0722-13.8684-20.4591
61.1963-0.92410.14635.4358-3.04891.7983-0.09360.0627-0.2077-0.08570.13050.0980.0622-0.1355-0.07210.16850.0079-0.01540.1408-0.01780.1453-13.5749-2.7022-17.263
71.3022-0.89120.2943.0895-3.16073.57760.10320.20260.1676-0.0093-0.15660.0191-0.16870.07160.03080.1644-0.003-0.04460.1618-0.00540.1603-9.50518.6237-27.4151
81.9081-0.0927-0.15033.8139-5.18017.0496-0.10440.13780.0794-0.2953-0.0354-0.15450.1853-0.02930.11290.1927-0.0144-0.02610.1545-0.01780.1201-5.80763.4399-22.2923
96.52042.9687-0.53373.9288-0.67781.15170.0983-0.2463-0.36570.6371-0.1045-0.0373-0.1447-0.034-0.01380.1757-0.00060.05770.12330.00480.1366-7.57032.5036-1.4485
104.1705-0.41-4.92880.04110.48365.80440.0775-0.43240.51110.14840.116-0.0876-0.05910.5027-0.36020.1476-0.0297-0.00160.1703-0.01890.1538-1.848512.6455-5.5713
114.13442.4960.41824.73510.22451.5827-0.16430.25540.147-0.43930.23360.6924-0.008-0.2160.03670.1799-0.0142-0.0350.16760.01670.2531-24.59630.5606-8.0004
122.71321.6583-0.01723.0570.47010.9050.0872-0.26420.10860.1214-0.14170.13010.01110.1292-0.00410.18210.00920.02350.1519-0.00380.1423-14.64335.4978-0.2638
132.53332.823-1.24914.8372-1.98432.20380.1009-0.10.03240.1063-0.08380.28380.05580.0924-0.01380.1536-0.00210.03210.1167-0.00330.148-19.3294-2.1366-2.9646
143.3663-2.49210.38162.85680.83678.0390.03580.05340.31210.091-0.0166-0.0368-0.1788-0.07-0.06290.1191-0.00710.00990.08920.01120.1567-8.765715.4925-14.3034
153.94131.2992-3.66663.3531-0.44734.1538-0.0062-0.00890.0114-0.9016-0.0661-0.33730.25440.10580.05180.19140.01320.04740.1280.01440.1169-15.6863-2.705-10.3324
161.9433-1.01183.57083.67770.88129.1610.4298-0.0535-0.3305-0.05720.1304-0.63090.14610.6443-0.30660.2879-0.00130.14660.25370.03420.5395-14.3298-14.7938-0.6367
172.28961.6711-2.0073.4753-4.71916.92960.0024-0.1211-0.1623-0.1303-0.1692-0.0180.21450.1790.07840.14490.00870.00680.1238-0.01050.1334-6.13590.0311-8.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 18 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 48 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 58 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 82 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 97 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 98 through 112 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 113 through 125 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 18 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 19 through 28 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 40 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 58 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 59 through 74 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 90 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 97 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 98 through 103 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 104 through 124 )B0

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