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- PDB-5ezp: Human transthyretin (TTR) complexed with 4-hydroxy-chalcone -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ezp
TitleHuman transthyretin (TTR) complexed with 4-hydroxy-chalcone
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Human transthyretin (TTR) / chalcone / inhibitor complex / new crystal polymorph
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
4-hydroxy-chalcone / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPolsinelli, I. / Nencetti, S. / Shepard, W.E. / Orlandini, E. / Stura, E.A.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: A new crystal form of human transthyretin obtained with a curcumin derived ligand.
Authors: Polsinelli, I. / Nencetti, S. / Shepard, W. / Ciccone, L. / Orlandini, E. / Stura, E.A.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
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
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,09514
Polymers106,9118
Non-polymers1,1836
Water5,927329
1
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1297
Polymers53,4564
Non-polymers6733
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-44 kcal/mol
Surface area20160 Å2
MethodPISA
2
E: Transthyretin
F: Transthyretin
G: Transthyretin
H: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9667
Polymers53,4564
Non-polymers5113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-44 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.480, 62.480, 238.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASNASNAA11 - 1246 - 119
21PROPROASNASNBB11 - 1246 - 119
12PROPROASNASNAA11 - 1246 - 119
22PROPROASNASNCC11 - 1246 - 119
13PROPROASNASNAA11 - 1246 - 119
23PROPROASNASNDD11 - 1246 - 119
14PROPROASNASNAA11 - 1246 - 119
24PROPROASNASNEE11 - 1246 - 119
15PROPROASNASNAA11 - 1246 - 119
25PROPROASNASNFF11 - 1246 - 119
16PROPROASNASNAA11 - 1246 - 119
26PROPROASNASNGG11 - 1246 - 119
17PROPROTHRTHRAA11 - 1236 - 118
27PROPROTHRTHRHH11 - 1236 - 118
18PROPROGLUGLUBB11 - 1276 - 122
28PROPROGLUGLUCC11 - 1276 - 122
19PROPROPROPROBB11 - 1256 - 120
29PROPROPROPRODD11 - 1256 - 120
110PROPROLYSLYSBB11 - 1266 - 121
210PROPROLYSLYSEE11 - 1266 - 121
111PROPROGLUGLUBB11 - 1276 - 122
211PROPROGLUGLUFF11 - 1276 - 122
112PROPROLYSLYSBB11 - 1266 - 121
212PROPROLYSLYSGG11 - 1266 - 121
113PROPROTHRTHRBB11 - 1236 - 118
213PROPROTHRTHRHH11 - 1236 - 118
114PROPROPROPROCC11 - 1256 - 120
214PROPROPROPRODD11 - 1256 - 120
115PROPROLYSLYSCC11 - 1266 - 121
215PROPROLYSLYSEE11 - 1266 - 121
116PROPROGLUGLUCC11 - 1276 - 122
216PROPROGLUGLUFF11 - 1276 - 122
117PROPROLYSLYSCC11 - 1266 - 121
217PROPROLYSLYSGG11 - 1266 - 121
118PROPROTHRTHRCC11 - 1236 - 118
218PROPROTHRTHRHH11 - 1236 - 118
119PROPROPROPRODD11 - 1256 - 120
219PROPROPROPROEE11 - 1256 - 120
120PROPROPROPRODD11 - 1256 - 120
220PROPROPROPROFF11 - 1256 - 120
121PROPROPROPRODD11 - 1256 - 120
221PROPROPROPROGG11 - 1256 - 120
122PROPROTHRTHRDD11 - 1236 - 118
222PROPROTHRTHRHH11 - 1236 - 118
123PROPROLYSLYSEE11 - 1266 - 121
223PROPROLYSLYSFF11 - 1266 - 121
124CYSCYSLYSLYSEE10 - 1265 - 121
224CYSCYSLYSLYSGG10 - 1265 - 121
125PROPROTHRTHREE11 - 1236 - 118
225PROPROTHRTHRHH11 - 1236 - 118
126PROPROLYSLYSFF11 - 1266 - 121
226PROPROLYSLYSGG11 - 1266 - 121
127PROPROTHRTHRFF11 - 1236 - 118
227PROPROTHRTHRHH11 - 1236 - 118
128PROPROTHRTHRGG11 - 1236 - 118
228PROPROTHRTHRHH11 - 1236 - 118

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13363.935 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766
#2: Chemical
ChemComp-IPJ / 4-hydroxy-chalcone


Mass: 224.255 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H12O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 5mg/ML in 0.05 M NaCl, 0.025 M Na acetate, pH 5.5 and 0.001 M 4-hydroxychalcone Reservoir: 30% PEG4K, 0.1M Tris-HCl, pH 8.5 4 boosts (5 M NaCl) Cryoprotectant: CryoSol SM1, 25% PEG ...Details: Protein: 5mg/ML in 0.05 M NaCl, 0.025 M Na acetate, pH 5.5 and 0.001 M 4-hydroxychalcone Reservoir: 30% PEG4K, 0.1M Tris-HCl, pH 8.5 4 boosts (5 M NaCl) Cryoprotectant: CryoSol SM1, 25% PEG 4K, 0.1 M (Na acetate, ADA, Bicine) Buffer 20% acid / 80% basic 0.01 M ligand.
PH range: 7-8.5 / Temp details: Air conditioned room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo-nozzle
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2015
Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut Si[111] crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 35806 / Num. obs: 35643 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Rsym value: 0.19 / Net I/σ(I): 8.52
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 5.15 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 1.15 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PMF

4pmf


Resolution: 2.5→44.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 29.486 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.875 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24467 1783 5 %RANDOM
Rwork0.20997 ---
obs0.21173 33860 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.257 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å2-0 Å2
2---1.14 Å2-0 Å2
3---3.69 Å2
Refinement stepCycle: 1 / Resolution: 2.5→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 89 329 7675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197613
X-RAY DIFFRACTIONr_bond_other_d0.0140.027019
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.95810377
X-RAY DIFFRACTIONr_angle_other_deg2.302316222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6623.861316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.771151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1411533
X-RAY DIFFRACTIONr_chiral_restr0.1010.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218563
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021722
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_it2.3143.1233771
X-RAY DIFFRACTIONr_mcbond_other2.3133.1233770
X-RAY DIFFRACTIONr_mcangle_it4.0024.6664712
X-RAY DIFFRACTIONr_mcangle_other4.0014.6664713
X-RAY DIFFRACTIONr_scbond_it2.6693.5813842
X-RAY DIFFRACTIONr_scbond_other2.6693.5833843
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4555.2115666
X-RAY DIFFRACTIONr_long_range_B_refined7.53326.0537995
X-RAY DIFFRACTIONr_long_range_B_other7.53326.0657996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A122000.1
12B122000.1
21A122480.11
22C122480.11
31A120880.1
32D120880.1
41A122580.1
42E122580.1
51A124620.09
52F124620.09
61A125160.08
62G125160.08
71A121820.11
72H121820.11
81B122740.13
82C122740.13
91B119140.12
92D119140.12
101B119680.13
102E119680.13
111B123340.11
112F123340.11
121B123680.1
122G123680.1
131B119840.12
132H119840.12
141C120220.12
142D120220.12
151C122260.13
152E122260.13
161C126360.11
162F126360.11
171C125200.11
172G125200.11
181C121080.12
182H121080.12
191D120700.11
192E120700.11
201D122340.11
202F122340.11
211D121980.11
212G121980.11
221D119740.12
222H119740.12
231E123960.11
232F123960.11
241E124880.12
242G124880.12
251E119980.12
252H119980.12
261F127480.09
262G127480.09
271F121940.11
272H121940.11
281G126020.11
282H126020.11
LS refinement shellResolution: 2.504→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 124 -
Rwork0.384 2356 -
obs--95.68 %
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)
10.239-0.4284-0.0750.77740.1620.97770.03520.0463-0.0353-0.084-0.05820.06030.0911-0.11910.02310.28230.09160.01870.2589-0.0080.007643.125427.511-12.1357
20.0898-0.1423-0.08590.24210.09120.9010.03830.06180.0609-0.0104-0.0844-0.1012-0.01240.23490.04610.23650.08120.03950.31190.06860.05659.441638.5477-6.9382
30.778-0.2270.25880.6323-0.1040.8631-0.0652-0.0038-0.00430.1280.0603-0.1162-0.11210.00950.00490.3340.10080.00180.188-0.01510.02750.420739.966117.2466
40.7675-0.89410.0471.1173-0.28610.7663-0.09060.0083-0.07550.0840.07090.08490.153-0.15460.01970.30850.060.06720.25010.00490.019336.645725.088112.5574
50.2579-0.12660.00892.03350.04720.74590.06060.07290.128-0.0939-0.1079-0.07320.01810.27790.04730.27710.06740.03110.24560.05650.066273.05249.883829.5876
60.3576-0.0640.21680.6333-0.43490.39320.08070.0035-0.0265-0.0559-0.04560.0310.0365-0.0099-0.03520.32650.08680.0070.2122-0.01030.005452.64155.271824.7162
70.13420.05550.15810.2977-0.31010.76580.03550.0198-0.03470.1554-0.0929-0.0911-0.07740.07140.05750.4015-0.0168-0.05070.19920.02650.030568.13964.719353.7795
80.3874-0.2216-0.10770.3219-0.3471.21890.1293-0.0611-0.05160.00820.03490.09530.063-0.1373-0.16420.387-0.0401-0.01210.20740.03810.034749.8819-3.571248.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 125
2X-RAY DIFFRACTION2B11 - 127
3X-RAY DIFFRACTION3C11 - 127
4X-RAY DIFFRACTION4D11 - 126
5X-RAY DIFFRACTION5E6 - 127
6X-RAY DIFFRACTION6F11 - 127
7X-RAY DIFFRACTION7G10 - 127
8X-RAY DIFFRACTION8H11 - 124

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