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- PDB-2xn3: Crystal structure of thyroxine-binding globulin complexed with me... -

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Basic information

Entry
Database: PDB / ID: 2xn3
TitleCrystal structure of thyroxine-binding globulin complexed with mefenamic acid
Components(THYROXINE-BINDING GLOBULIN) x 2
KeywordsTRANSPORT / CLEAVED PROTEIN
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
2-[(2,3-DIMETHYLPHENYL)AMINO]BENZOIC ACID / Thyroxine-binding globulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsQi, X. / Yan, Y. / Wei, Z. / Zhou, A.
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
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: THYROXINE-BINDING GLOBULIN
B: THYROXINE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2463
Polymers43,0042
Non-polymers2411
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-36.8 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.835, 41.624, 56.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein THYROXINE-BINDING GLOBULIN / T4-BINDING GLOBULIN / SERPIN A7


Mass: 38399.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-375 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 346-355 OF TBG WERE REPLACED BY GAMFLEAIPRS
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05543
#2: Protein/peptide THYROXINE-BINDING GLOBULIN / T4-BINDING GLOBULIN / SERPIN A7


Mass: 4605.383 Da / Num. of mol.: 1 / Fragment: RESIDUES 377-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05543
#3: Chemical ChemComp-ID8 / 2-[(2,3-DIMETHYLPHENYL)AMINO]BENZOIC ACID / MEFENAMIC ACID


Mass: 241.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 366 TO GLY ENGINEERED RESIDUE IN CHAIN A, VAL 367 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ALA 366 TO GLY ENGINEERED RESIDUE IN CHAIN A, VAL 367 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 368 TO MET ENGINEERED RESIDUE IN CHAIN A, GLU 369 TO PHE ENGINEERED RESIDUE IN CHAIN A, VAL 370 TO LEU ENGINEERED RESIDUE IN CHAIN A, LEU 372 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 373 TO ILE ENGINEERED RESIDUE IN CHAIN A, ASP 374 TO PRO ENGINEERED RESIDUE IN CHAIN A, GLN 375 TO ARG

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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: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5.4 / Details: 20% PEG3350, PH 5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→21.97 Å / Num. obs: 24692 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.3 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RIV

2riv


Resolution: 2.09→86.39 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.626 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD PDB / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 1254 5.1 %RANDOM
Rwork0.21038 ---
obs0.21284 23353 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--3.2 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.09→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 18 130 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223017
X-RAY DIFFRACTIONr_bond_other_d0.0020.022009
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9674083
X-RAY DIFFRACTIONr_angle_other_deg0.90434944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17225.156128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.03158
X-RAY DIFFRACTIONr_chiral_restr0.070.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213304
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02587
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_it0.6291.51859
X-RAY DIFFRACTIONr_mcbond_other0.1221.5746
X-RAY DIFFRACTIONr_mcangle_it1.17223010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6931158
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6984.51072
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 71 -
Rwork0.251 1610 -
obs--95.57 %
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)
11.70510.2358-0.79860.7072-0.08171.721-0.03830.09730.0228-0.0890.0399-0.0398-0.00570.2393-0.00160.0369-0.0075-0.01450.06680.00250.04724.020612.152422.9725
23.32580.2101-1.54731.3805-0.55773.54990.07390.0323-0.1180.02140.041-0.0380.00230.1801-0.11490.0660.0004-0.0030.0183-0.00970.123715.793110.055834.3404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 355
2X-RAY DIFFRACTION2B362 - 395

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