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- PDB-7q3i: Human Transthyretin expressed in Vibrio natriegens -

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Basic information

Entry
Database: PDB / ID: 7q3i
TitleHuman Transthyretin expressed in Vibrio natriegens
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / hormone binding / Transthyretin
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 / Resolution: 1.55 Å
AuthorsHild Walett, O. / Hammarstrom, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2019-04405 Sweden
CitationJournal: To Be Published
Title: Human Transthyretin expressed in Vibrio natriegens
Authors: Hild Walett, O. / Hammarstrom, P.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Transthyretin
BBB: Transthyretin


Theoretical massNumber of molelcules
Total (without water)27,7292
Polymers27,7292
Non-polymers00
Water2,954164
1
AAA: Transthyretin
BBB: Transthyretin

AAA: Transthyretin
BBB: Transthyretin


  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
  • 55.5 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)55,4584
Polymers55,4584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6150 Å2
ΔGint-43 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.439, 62.896, 85.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11AAA-237-

HOH

21BBB-241-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 10 - 124 / Label seq-ID: 11 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13864.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Evidence for an ill-defined ligand in the t4 binding pocket.
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Vibrio natriegens (bacteria) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 11.6 mg/mL protein in PBS pH 7.4 mixed 1:1 with MgFormate 0.1 M, 24 % PEG1000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979499 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.55→50.683 Å / Num. obs: 33691 / % possible obs: 99 % / Redundancy: 11.5 % / Biso Wilson estimate: 20.267 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.048 / Χ2: 0.78 / Net I/σ(I): 21.7
Reflection shellResolution: 1.55→8.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1472 / CC1/2: 0.772 / Rpim(I) all: 0.437 / Rrim(I) all: 0.751 / Χ2: 0.53 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house E. coli TTR structure

Resolution: 1.55→50.683 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.227 1666 4.954 %
Rwork0.1819 31966 -
all0.184 --
obs-33632 98.848 %
Solvent computationIon probe radii: 0 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 5 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 23.007 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---0.461 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 0 164 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131711
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171517
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.6412348
X-RAY DIFFRACTIONr_angle_other_deg2.531.5613483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1525228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53822.32156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0515219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.417154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021940
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02366
X-RAY DIFFRACTIONr_nbd_refined0.1870.2268
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.21263
X-RAY DIFFRACTIONr_nbtor_refined0.180.2837
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.214
X-RAY DIFFRACTIONr_nbd_other0.1730.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.211
X-RAY DIFFRACTIONr_mcbond_it1.7061.795918
X-RAY DIFFRACTIONr_mcbond_other1.7031.792917
X-RAY DIFFRACTIONr_mcangle_it1.8582.6891144
X-RAY DIFFRACTIONr_mcangle_other1.8582.6911145
X-RAY DIFFRACTIONr_scbond_it2.1741.998793
X-RAY DIFFRACTIONr_scbond_other2.1762794
X-RAY DIFFRACTIONr_scangle_it2.2652.9031204
X-RAY DIFFRACTIONr_scangle_other2.2612.9021204
X-RAY DIFFRACTIONr_lrange_it2.38336.0096753
X-RAY DIFFRACTIONr_lrange_other2.27735.2586608
X-RAY DIFFRACTIONr_rigid_bond_restr7.86433228
X-RAY DIFFRACTIONr_ncsr_local_group_10.1120.053000
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.112140.05007
12BBBX-RAY DIFFRACTIONLocal ncs0.112140.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.55-1.590.2521050.2721050.26924600.8350.82589.83740.246
1.59-1.6340.291250.2221880.22424270.8280.86695.30280.196
1.634-1.6810.2541190.19322260.19623530.8970.90399.660.168
1.681-1.7330.2541120.1821480.18422610.9110.92499.95580.154
1.733-1.790.2990.16321220.16522210.9290.9421000.138
1.79-1.8520.2161220.13820480.14221710.9370.96199.95390.116
1.852-1.9220.206970.1419450.14320430.9540.96399.9510.119
1.922-20.1811010.13519100.13720110.9570.9671000.116
2-2.0890.206920.14218130.14619060.9540.96299.94750.126
2.089-2.1910.197940.13517420.13818370.9550.9799.94560.12
2.191-2.3090.182950.13516630.13817590.9490.96899.94310.124
2.309-2.4490.255880.15115870.15616760.9310.95699.94030.14
2.449-2.6180.204730.16114910.16415650.9460.95599.93610.149
2.618-2.8270.205660.15914030.16114700.9510.96299.9320.149
2.827-3.0960.232680.17112940.17413630.9440.95599.92660.164
3.096-3.4590.184440.17911880.17912330.9620.95799.91890.173
3.459-3.9920.192500.18110490.18111000.9560.95399.90910.178
3.992-4.8810.238510.1748930.1779460.9410.95899.78860.176
4.881-6.8710.263360.2547200.2547570.9060.90999.86790.253
6.871-50.6830.401280.4164310.4154630.8590.77999.13610.411
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)
10.76540.0240.50430.5370.20331.1121-0.0497-0.06940.0434-0.05240.0683-0.0041-0.0741-0.0349-0.01850.0092-0.0061-0.00160.0744-0.0130.037920.80425.15112.972
20.30250.2723-0.11250.4621-0.45221.0076-0.0185-0.0266-0.0544-0.04350.03350.010.06670.0672-0.0150.0079-0.0060.00790.09150.01910.068224.1846.54912.493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA10 - 124
2X-RAY DIFFRACTION2ALLBBB10 - 124

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