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- PDB-4der: Crystal Structure of the Wild Type TTR Binding Apigenin (TTRwt:API) -

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Basic information

Entry
Database: PDB / ID: 4der
TitleCrystal Structure of the Wild Type TTR Binding Apigenin (TTRwt:API)
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / beta sandwich / amyloidosis
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
Chem-AGI / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTrivella, D.B.B. / Polikarpov, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Flavonoid interactions with human transthyretin: Combined structural and thermodynamic analysis.
Authors: Trivella, D.B. / Dos Reis, C.V. / Lima, L.M. / Foguel, D. / Polikarpov, I.
History
DepositionJan 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0395
Polymers25,4062
Non-polymers6333
Water2,234124
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,07810
Polymers50,8134
Non-polymers1,2656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6190 Å2
ΔGint-48 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.152, 85.132, 64.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

AGI

21A-201-

AGI

31A-201-

AGI

41A-201-

AGI

51A-201-

AGI

61B-201-

AGI

71B-201-

AGI

81B-201-

AGI

91B-201-

AGI

101B-201-

AGI

111B-201-

AGI

121A-335-

HOH

131B-320-

HOH

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Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12703.217 Da / Num. of mol.: 2 / Fragment: UNP residues 30-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-AGI / 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one / Apigenin


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 7.5, 28% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4589 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2009
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4589 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 20996 / Num. obs: 19821 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.065 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.70.50614801.156172.5
1.92-1.994.30.33816750.987180.8
1.99-2.084.70.29618911.067192.1
2.08-2.195.10.23520151.031198.1
2.19-2.335.30.20920961.0661100
2.33-2.515.40.17720891.0841100
2.51-2.765.40.14120871.0991100
2.76-3.165.50.11821021.0331100
3.16-3.985.40.06721431.1111100
3.98-305.20.04422431.035199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CFM

3cfm


Resolution: 1.9→21.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.519 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 964 5.2 %RANDOM
Rwork0.1893 ---
all0.1917 19632 --
obs0.1917 18668 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.92 Å2 / Biso mean: 27.1959 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 46 124 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222022
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9752789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54824.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.274157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211583
X-RAY DIFFRACTIONr_mcbond_it0.8921.51242
X-RAY DIFFRACTIONr_mcangle_it1.62222040
X-RAY DIFFRACTIONr_scbond_it2.243780
X-RAY DIFFRACTIONr_scangle_it3.4874.5739
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 65 -
Rwork0.258 1031 -
all-1096 -
obs--77.57 %

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