[English] 日本語
Yorodumi
- PDB-2xn5: Crystal structure of thyroxine-binding globulin complexed with Fu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xn5
TitleCrystal structure of thyroxine-binding globulin complexed with Furosemide
Components(THYROXINE-BINDING ...) 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
Chem-FUN / Thyroxine-binding globulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THYROXINE-BINDING GLOBULIN
B: THYROXINE-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,91211
Polymers43,1732
Non-polymers7399
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-62.4 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.880, 42.150, 56.190
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-2201-

HOH

-
Components

-
THYROXINE-BINDING ... , 2 types, 2 molecules AB

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


Mass: 39145.879 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-380 / 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: 4026.811 Da / Num. of mol.: 1 / Fragment: RESIDUES 381-415
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

-
Non-polymers , 4 types, 282 molecules

#3: Chemical ChemComp-FUN / 5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID / Furosemide / Furosemide


Mass: 330.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2O5S / Comment: medication*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Details

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, GLU 371 TO GLU 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 ENGINEERED RESIDUE IN CHAIN A, PRO 376 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 377 TO ILE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 1.7→34.58 Å / Num. obs: 40382 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 71.1

-
Processing

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

2riv


Resolution: 1.7→86.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.181 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23208 2166 5.1 %RANDOM
Rwork0.2043 ---
obs0.20574 40382 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.798 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--2.43 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→86.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 41 273 3265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223115
X-RAY DIFFRACTIONr_bond_other_d0.0010.022081
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9714224
X-RAY DIFFRACTIONr_angle_other_deg0.79135131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6625.349129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70715557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.598157
X-RAY DIFFRACTIONr_chiral_restr0.0670.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it0.4611.51921
X-RAY DIFFRACTIONr_mcbond_other0.11.5769
X-RAY DIFFRACTIONr_mcangle_it0.86923122
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41931194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2594.51098
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 103 -
Rwork0.327 1956 -
obs--61.23 %
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)
10.9-0.1508-0.52740.47670.01761.1815-0.0011-0.0030.00810.02790.01280.0112-0.0252-0.1004-0.01170.0277-0.0005-0.01130.01260.00280.0167-24.2219-8.97645.2317
20.74070.227-0.57750.7330.15653.23780.08490.0286-0.0402-0.01850.0132-0.04480.0330.023-0.09810.04030.01380.00040.00540.00060.038-15.7703-11.0705-5.9541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 355
2X-RAY DIFFRACTION2B362 - 398

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more