[English] 日本語
Yorodumi
- PDB-2qgd: Human transthyretin (TTR) complexed with 2-(3,5-Dibromo-4-hydroxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qgd
TitleHuman transthyretin (TTR) complexed with 2-(3,5-Dibromo-4-hydroxyphenyl)benzoxazole
ComponentsTransthyretin
KeywordsHormone/Growth Factor / Transthyretin / Tetramer / Amyloidogenesis Inhibitors / Hormone-Growth Factor COMPLEX
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) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / 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
4-(1,3-BENZOXAZOL-2-YL)-2,6-DIBROMOPHENOL / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsConnelly, S. / Wilson, I.A.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Biochemical and structural evaluation of highly selective 2-arylbenzoxazole-based transthyretin amyloidogenesis inhibitors.
Authors: Johnson, S.M. / Connelly, S. / Wilson, I.A. / Kelly, J.W.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2934
Polymers27,5552
Non-polymers7382
Water2,558142
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5858
Polymers55,1094
Non-polymers1,4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8690 Å2
ΔGint-61 kcal/mol
Surface area18590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.945, 85.001, 65.097
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-200-

MR5

21A-200-

MR5

31A-200-

MR5

41A-200-

MR5

51B-201-

MR5

61B-201-

MR5

71B-201-

MR5

-
Components

#1: Protein Transthyretin / Prealbumin / TBPA / TTR / ATTR


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766
#2: Chemical ChemComp-MR5 / 4-(1,3-BENZOXAZOL-2-YL)-2,6-DIBROMOPHENOL / 2-(3,5-DIBROMO-4-HYDROXYPHENYL)BENZOXAZOLE


Mass: 369.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H7Br2NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method. Crystals ...Details: The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.912 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionRedundancy: 14.5 % / Av σ(I) over netI: 11 / Number: 557366 / Rmerge(I) obs: 0.062 / Χ2: 1.05 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 38438 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.75098.810.0330.99713.2
2.943.710010.0381.03214.1
2.562.9410010.050.98814.5
2.332.5610010.0631.04114.7
2.162.3310010.0660.99614.7
2.042.1610010.0771.06514.7
1.932.0410010.0931.05614.7
1.851.9310010.1221.1114.7
1.781.8510010.1821.08414.7
1.721.7810010.2481.08414.7
1.661.7210010.3131.08714.7
1.621.6610010.3751.06414.6
1.571.6210010.4411.06514.6
1.531.5710010.5411.05714.6
1.51.5310010.671.04714.5
ReflectionResolution: 1.5→50 Å / Num. obs: 38438 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.062 / Χ2: 1.052 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2511 / Rsym value: 0.67 / Χ2: 1.047 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Transthyretin PDB 2FBR

2fbr


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.188 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1924 5 %RANDOM
Rwork0.16 ---
obs0.162 38380 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 36 142 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221973
X-RAY DIFFRACTIONr_bond_other_d0.0030.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9682718
X-RAY DIFFRACTIONr_angle_other_deg0.9323.0013171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06723.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98615310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4121510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.1990.2325
X-RAY DIFFRACTIONr_nbd_other0.2030.21248
X-RAY DIFFRACTIONr_nbtor_refined0.180.2922
X-RAY DIFFRACTIONr_nbtor_other0.0880.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.212
X-RAY DIFFRACTIONr_mcbond_it2.5211.51549
X-RAY DIFFRACTIONr_mcbond_other0.9251.5482
X-RAY DIFFRACTIONr_mcangle_it3.0221967
X-RAY DIFFRACTIONr_scbond_it4.4193945
X-RAY DIFFRACTIONr_scangle_it5.3854.5736
X-RAY DIFFRACTIONr_rigid_bond_restr2.28234113
X-RAY DIFFRACTIONr_sphericity_free9.9743142
X-RAY DIFFRACTIONr_sphericity_bonded4.78233203
LS refinement shellResolution: 1.5→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 122 -
Rwork0.15 2491 -
obs-2613 92.53 %

+
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