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- PDB-2qpf: Crystal Structure of Mouse Transthyretin -

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Basic information

Entry
Database: PDB / ID: 2qpf
TitleCrystal Structure of Mouse Transthyretin
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / amyloidogenesis / tetramer / Glycoprotein / Hormone / Retinol-binding / Secreted / Thyroid hormone / Vitamin A
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / negative regulation of glomerular filtration / hormone binding / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Neutrophil degranulation / hormone activity / protein-containing complex binding ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / negative regulation of glomerular filtration / hormone binding / molecular sequestering activity / phototransduction, visible light / retinoid metabolic process / Neutrophil degranulation / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsReixach, N. / Foss, T.R. / Santelli, E. / Pascual, J. / Kelly, J.W. / Buxbaum, J.N.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Human-Murine Transthyretin Heterotetramers Are Kinetically Stable and Non-amyloidogenic: A LESSON IN THE GENERATION OF TRANSGENIC MODELS OF DISEASES INVOLVING OLIGOMERIC PROTEINS.
Authors: Reixach, N. / Foss, T.R. / Santelli, E. / Pascual, J. / Kelly, J.W. / Buxbaum, J.N.
History
DepositionJul 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin


Theoretical massNumber of molelcules
Total (without water)110,6838
Polymers110,6838
Non-polymers00
Water6,251347
1
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,3424
Polymers55,3424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
MethodPISA
2
E: Transthyretin
F: Transthyretin

E: Transthyretin
F: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,3424
Polymers55,3424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6090 Å2
MethodPISA
3
G: Transthyretin
H: Transthyretin

G: Transthyretin
H: Transthyretin


Theoretical massNumber of molelcules
Total (without water)55,3424
Polymers55,3424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.511, 120.511, 113.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-228-

HOH

21F-154-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21A
12H
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: OCS / Beg label comp-ID: OCS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 10 - 123 / Label seq-ID: 11 - 124

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11GG
21AA
12HH
22CC

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transthyretin / Prealbumin


Mass: 13835.421 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttr / Plasmid: pMMHa / Production host: Escherichia coli (E. coli) / References: UniProt: P07309
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 2000 MME, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 60027 / Num. obs: 60024 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 32.5
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5935 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1dvq

1dvq


Resolution: 2.05→24.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.049 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24609 3033 5.1 %RANDOM
Rwork0.198 ---
obs0.20043 59951 99.93 %-
all-60088 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 0 347 7480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227367
X-RAY DIFFRACTIONr_bond_other_d0.0010.024823
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.94810047
X-RAY DIFFRACTIONr_angle_other_deg0.731311799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3455925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52723.564289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.099151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5281525
X-RAY DIFFRACTIONr_chiral_restr0.0640.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021527
X-RAY DIFFRACTIONr_nbd_refined0.1710.21037
X-RAY DIFFRACTIONr_nbd_other0.1760.24535
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23469
X-RAY DIFFRACTIONr_nbtor_other0.0790.23819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.44125896
X-RAY DIFFRACTIONr_mcbond_other1.09621870
X-RAY DIFFRACTIONr_mcangle_it4.07637474
X-RAY DIFFRACTIONr_scbond_it6.23243347
X-RAY DIFFRACTIONr_scangle_it7.82552571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1G670tight positional0.020.05
2H660tight positional0.020.05
1G802loose positional0.55
2H769loose positional0.475
1G670tight thermal1.225
2H660tight thermal1.285
1G802loose thermal2.9220
2H769loose thermal3.0420
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 210 -
Rwork0.279 4115 -
obs--99.88 %
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)
12.3853-1.00440.85184.6993-1.48442.8894-0.081-0.11330.40150.1316-0.1455-0.025-0.33690.01080.2265-0.2407-0.04860.0041-0.1932-0.0898-0.2096-45.004945.24565.6298
24.21350.67950.85212.79880.44322.26790.02540.26660.0985-0.2841-0.0972-0.5436-0.04070.58340.0717-0.19580.02580.1213-0.04880.0568-0.1868-32.087536.7045-7.6914
32.3678-0.0177-0.72662.9885-0.91854.1760.11-0.4463-0.16920.1953-0.01880.48050.3029-0.1353-0.0912-0.2367-0.06240.0051-0.15630.0046-0.1646-58.780522.46896.6622
42.99360.65621.60754.021.3173.90710.24640.1267-0.4709-0.297-0.0596-0.06520.60640.2945-0.1869-0.0570.1069-0.0385-0.21810.0108-0.1909-43.289412.912-1.7536
56.22430.42210.5592.9325-0.74023.25130.24290.24890.9442-0.05290.16320.788-0.1261-0.2921-0.4061-0.23540.02210.0874-0.2060.11770.1046-28.815429.8697-37.3093
64.51391.7591-1.17394.6695-1.55674.1671-0.26290.1192-0.824-0.20610.1912-0.11230.8944-0.02760.07170.08910.0345-0.026-0.256-0.046-0.1123-15.26636.9021-40.0596
74.231-0.7577-2.34072.9074-0.436412.98650.1075-0.2489-0.7372-0.1834-0.22020.88411.0591-3.09320.11270.3291-0.4827-0.14070.8173-0.0290.08781.261221.79860.0064
83.6825-1.11560.85525.6215-1.64289.08170.1509-0.50140.8667-0.468-0.1053-0.0021-2.4256-0.1323-0.04560.9594-0.21290.18960.0987-0.2192-0.045114.530144.78642.8574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1249 - 125
2X-RAY DIFFRACTION2BB9 - 12310 - 124
3X-RAY DIFFRACTION3CC8 - 1249 - 125
4X-RAY DIFFRACTION4DD10 - 12311 - 124
5X-RAY DIFFRACTION5EE9 - 12410 - 125
6X-RAY DIFFRACTION6FF9 - 12410 - 125
7X-RAY DIFFRACTION7GG10 - 12311 - 124
8X-RAY DIFFRACTION8HH10 - 12311 - 124

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