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- PDB-4x30: Crystal structure of human Thyroxine-binding globulin complexed w... -

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Basic information

Entry
Database: PDB / ID: 4x30
TitleCrystal structure of human Thyroxine-binding globulin complexed with thyroine at 1.55 Angstrom resolution
ComponentsThyroxine-binding globulin
KeywordsTRANSPORT PROTEIN / TBG / Thyroxine-binding globulin / serpin / thyroxine / cation Pi interaction / hormone release
Function / homology
Function and homology information


thyroid hormone transport / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / 3,5,3',5'-TETRAIODO-L-THYRONINE / Thyroxine-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsQi, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170724 China
nsfc31370727 China
CitationJournal: To Be Published
Title: Crystal structure of human Thyroxine-binding globulin complexed with thyroine at 1.55 Angstrom resolution
Authors: Qi, X. / Zhou, A.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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: Thyroxine-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2137
Polymers44,1481
Non-polymers1,0656
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.460, 65.460, 202.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

21A-622-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thyroxine-binding globulin / / Serpin A7 / T4-binding globulin


Mass: 44147.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pSUMO3 / Details (production host): pSUMO3-TBG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P05543

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Non-polymers , 6 types, 371 molecules

#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE / Levothyroxine


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4 / Details: PEG3350, (NH4)2SO4, NaCl, Tris-HCl / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→34.5 Å / Num. obs: 64376 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
MOSFLMdata processing
PHASERphasing
SCALAdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ceo

2ceo


Resolution: 1.55→34.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.058 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 3260 5.1 %RANDOM
Rwork0.18333 ---
obs0.18442 60985 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 42 365 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193148
X-RAY DIFFRACTIONr_bond_other_d0.0010.023023
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9694277
X-RAY DIFFRACTIONr_angle_other_deg0.71336987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6825.522134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85415564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.578157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
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_it0.9721.5911548
X-RAY DIFFRACTIONr_mcbond_other0.9671.5891547
X-RAY DIFFRACTIONr_mcangle_it1.6362.3791953
X-RAY DIFFRACTIONr_mcangle_other1.6372.3811954
X-RAY DIFFRACTIONr_scbond_it1.311.7721600
X-RAY DIFFRACTIONr_scbond_other1.3081.7721600
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1142.5922324
X-RAY DIFFRACTIONr_long_range_B_refined5.27114.2033813
X-RAY DIFFRACTIONr_long_range_B_other5.27114.2063814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 272 -
Rwork0.321 4468 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -5.1688 Å / Origin y: 21.687 Å / Origin z: -25.3023 Å
111213212223313233
T0.0255 Å2-0.0004 Å2-0.0102 Å2-0.0114 Å20.0015 Å2--0.0133 Å2
L0.0767 °2-0.1165 °20.0948 °2-0.3752 °2-0.4285 °2--0.7969 °2
S0.0095 Å °0.0213 Å °0.0036 Å °0.0449 Å °-0.0323 Å °-0.0425 Å °-0.072 Å °0.0401 Å °0.0228 Å °

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