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- PDB-2riv: Crystal structure of the reactive loop cleaved human Thyroxine Bi... -

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Basic information

Entry
Database: PDB / ID: 2riv
TitleCrystal structure of the reactive loop cleaved human Thyroxine Binding Globulin
Components(Thyroxine-binding globulin) x 2
KeywordsSIGNALING PROTEIN / TBG / Serpin / cleaved / thyroxine binding globulin / thyroxine / Disease mutation / Glycoprotein / Secreted
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
Thyroxine-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhou, A. / Wei, Z. / Stanley, P.L.D. / Read, R.J. / Stein, P.E. / Carrell, R.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Allosteric modulation of hormone release from thyroxine and corticosteroid-binding globulins
Authors: Qi, X. / Loiseau, F. / Chan, W.L. / Yan, Y. / Wei, Z. / Milroy, L.G. / Myers, R.M. / Ley, S.V. / Read, R.J. / Carrell, R.W. / Zhou, A.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Thyroxine-binding globulin
B: Thyroxine-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4737
Polymers43,0042
Non-polymers4685
Water7,710428
1
A: Thyroxine-binding globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8676
Polymers38,3991
Non-polymers4685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thyroxine-binding globulin


Theoretical massNumber of molelcules
Total (without water)4,6051
Polymers4,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-65 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.136, 42.585, 55.989
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-454-

HOH

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Components

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


Mass: 38399.074 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 33-375
Source method: isolated from a genetically manipulated source
Details: Purified From the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS / References: UniProt: P05543
#2: Protein/peptide Thyroxine-binding globulin / TBG / T4-binding globulin / Serpin A7


Mass: 4605.383 Da / Num. of mol.: 1
Fragment: reactive loop cleaved TBG, C-teemingly domain, UNP residues 376-415
Source method: isolated from a genetically manipulated source
Details: Purified From the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS / References: UniProt: P05543
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REACTIVE LOOP P10-P1' CLEAVED CONFORMATION OF TBG WAS MUTATED TO GAMFLEAIPRS. THE FIRST ...THE REACTIVE LOOP P10-P1' CLEAVED CONFORMATION OF TBG WAS MUTATED TO GAMFLEAIPRS. THE FIRST RESIDUES, GAMFLEAIPR, ARE LOCATED AT C-TERMINAL IN CHAIN A AND THE LAST RESIDUE, S, IS LOCATED AT N-TERMINAL IN CHAIN B.

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.4
Details: 20% PEG 3350, 0.2M sodium sulphate, pH 7.4, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.5419 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.5→29.5 Å / Num. all: 64019 / Num. obs: 63059 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.9
Reflection shellResolution: 1.5→1.539 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 7.5 / Num. unique all: 3930 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMB

1qmb


Resolution: 1.5→29.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.768 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 7.5 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21401 3355 5.1 %RANDOM
Rwork0.18875 ---
obs0.19 63059 98.54 %-
all-63059 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 28 428 3391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223163
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9674315
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5935416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28425.368136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.044157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022346
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21476
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22207
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.51989
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2223160
X-RAY DIFFRACTIONr_scbond_it1.97431315
X-RAY DIFFRACTIONr_scangle_it3.034.51133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.55 216 -
Rwork0.422 3930 -
obs-3930 84.77 %
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)
10.55580.089-0.25020.3534-0.04370.8354-0.00350.02680.0177-0.03910.0141-0.0076-0.02610.1823-0.0107-0.0363-0.0055-0.0063-0.0367-0.0079-0.045524.275212.849922.546
21.4045-0.0879-0.06470.76460.1641.39460.0333-0.0264-0.01810.0311-0.02730.09960.03420.0779-0.006-0.0187-0.0027-0.0053-0.0634-0.0104-0.016216.168310.848734.0026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 3557 - 343
2X-RAY DIFFRACTION2BB362 - 3957 - 40

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