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- PDB-5dwp: Crystal Structure of human transthyretin (TTR) processed with the... -

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Basic information

Entry
Database: PDB / ID: 5dwp
TitleCrystal Structure of human transthyretin (TTR) processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsTransthyretin
KeywordsTRANSFERASE / transthyretin
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZander, U. / Cornaciu, I. / Forsyth, T. / Yee, A. / Marquez, J.A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Automated harvesting and processing of protein crystals through laser photoablation.
Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)25,4062
Polymers25,4062
Non-polymers00
Water4,396244
1
A: Transthyretin
B: Transthyretin

A: Transthyretin
B: Transthyretin


Theoretical massNumber of molelcules
Total (without water)50,8134
Polymers50,8134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)41.346, 62.521, 85.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-283-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSERAA20 - 10011 - 91
21VALVALSERSERBB20 - 10011 - 91
12ARGARGASNASNAA103 - 12494 - 115
22ARGARGASNASNBB103 - 12494 - 115

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.973425, 0.019498, 0.228176), (-0.017892, -0.999798, 0.009105), (0.228307, 0.004781, 0.973577)40.76681, -30.6403, -4.81098

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12703.217 Da / Num. of mol.: 2 / Fragment: UNP residues 31-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, 1.6 M ammonium sulfate, pH=5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.2→19.63 Å / Num. obs: 69740 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.2
Reflection shellResolution: 1.2→1.26 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVL

4pvl


Resolution: 1.2→19.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.017 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19559 3431 4.9 %RANDOM
Rwork0.16257 ---
obs0.16422 66062 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å20 Å2
2--0.93 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 0 244 2036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191974
X-RAY DIFFRACTIONr_bond_other_d0.0020.021804
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9422713
X-RAY DIFFRACTIONr_angle_other_deg2.49634185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.50923.53782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16615305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.27159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212281
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02448
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8471.389995
X-RAY DIFFRACTIONr_mcbond_other1.8321.381994
X-RAY DIFFRACTIONr_mcangle_it2.3922.0691263
X-RAY DIFFRACTIONr_mcangle_other2.4192.0771264
X-RAY DIFFRACTIONr_scbond_it3.8371.886979
X-RAY DIFFRACTIONr_scbond_other3.8351.891980
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.512.6491451
X-RAY DIFFRACTIONr_long_range_B_refined4.95213.7912301
X-RAY DIFFRACTIONr_long_range_B_other4.67312.9862181
X-RAY DIFFRACTIONr_rigid_bond_restr5.65833778
X-RAY DIFFRACTIONr_sphericity_free23.157554
X-RAY DIFFRACTIONr_sphericity_bonded9.30953904
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1405 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.755
loose thermal5.0110
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 248 -
Rwork0.314 4824 -
obs--99.16 %

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