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- PDB-4mas: High Resolution Structure of Wild Type Human Transthyretin in Com... -

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Basic information

Entry
Database: PDB / ID: 4mas
TitleHigh Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN/INHIBITOR / hormone / binding protein / hormone transport / thyroxine / retinol binding protein / TRANSPORT PROTEIN-INHIBITOR complex
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
3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsConnelly, S. / Bradbury, N.C. / Wilson, I.A.
CitationJournal: To be Published
Title: High Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol
Authors: Connelly, S. / Bradbury, N.C. / Wilson, I.A.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2034
Polymers27,5552
Non-polymers6482
Water3,225179
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4058
Polymers55,1094
Non-polymers1,2964
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8730 Å2
ΔGint-132 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.049, 85.020, 64.893
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-201-

PCQ

21A-201-

PCQ

31A-201-

PCQ

41A-201-

PCQ

51A-201-

PCQ

61A-201-

PCQ

71B-201-

PCQ

81B-201-

PCQ

91B-201-

PCQ

101B-201-

PCQ

111B-201-

PCQ

121B-201-

PCQ

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-PCQ / 3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL


Mass: 323.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H6Cl4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, ...Details: 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, cryoprotectant: 1.395 M sodium citrate, pH 5.5, 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.22→35.873 Å / Num. obs: 70897 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.028 / Net I/σ(I): 27.6
Reflection shellResolution: 1.22→1.29 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 10085 / Rsym value: 0.515 / % possible all: 98.2

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Processing

Software
NameVersionClassification
autoXDSdata collection
PHASERphasing
REFMAC5.6.0117refinement
autoXDSdata reduction
autoXDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FBR

2fbr


Resolution: 1.22→35.873 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.038 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17339 3580 5.1 %RANDOM
Rwork0.15053 ---
obs0.15168 67215 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.22→35.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 36 179 1997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022027
X-RAY DIFFRACTIONr_bond_other_d0.0010.021320
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9662800
X-RAY DIFFRACTIONr_angle_other_deg0.9523.0023255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93124.25387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.792159
X-RAY DIFFRACTIONr_chiral_restr0.10.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212339
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02422
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.68433345
X-RAY DIFFRACTIONr_sphericity_free30.197557
X-RAY DIFFRACTIONr_sphericity_bonded13.68753403
LS refinement shellResolution: 1.22→1.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 232 -
Rwork0.308 4515 -
obs-4515 98.2 %

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