[English] 日本語
Yorodumi
- PDB-1nr2: High resolution crystal structures of thymus and activation-regul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nr2
TitleHigh resolution crystal structures of thymus and activation-regulated chemokine
ComponentsThymus and activation-regulated chemokine
KeywordsCYTOKINE / TARC / chemokine / CC-chemokine / chemotaxis
Function / homology
Function and homology information


chemokine activity / Chemokine receptors bind chemokines / chemotaxis / cell-cell signaling / immune response / inflammatory response / signaling receptor binding / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 17
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsAsojo, O.A. / Boulegue, C. / Hoover, D.M. / Lu, W. / Lubkowski, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structures of thymus and activation-regulated chemokine (TARC).
Authors: Asojo, O.A. / Boulegue, C. / Hoover, D.M. / Lu, W. / Lubkowski, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray studies of thymus and activation-regulated chemokine
Authors: Asojo, O.A. / Hoover, D. / Boulegue, C. / Cater, S. / Lu, W. / Lubkowski, J.
History
DepositionJan 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymus and activation-regulated chemokine
B: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)16,1932
Polymers16,1932
Non-polymers00
Water4,053225
1
A: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)8,0961
Polymers8,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)8,0961
Polymers8,0961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.772, 47.772, 58.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Cell settingtetragonal
Space group name H-MP41

-
Components

#1: Protein Thymus and activation-regulated chemokine / Small inducible cytokine A17 / CCL17 / CC chemokine TARC / T cell-directed CC


Mass: 8096.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q92583
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17M ammonium acetate, 0.085M trisodium citrate, 25.5% PEG 4000, 15% w/v glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 285 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
20.17 Mammonium acetate1reservoir
30.085 Mtrisodium citrate1reservoirpH5.6
425.5 %(w/v)PEG40001reservoir
515 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2002
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→10 Å / Num. all: 6647 / Num. obs: 6647 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.064 / Net I/σ(I): 19
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.194 / Rsym value: 0.271 / % possible all: 93.4
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 93.5 % / Redundancy: 5.5 %
Reflection shell
*PLUS
% possible obs: 92.2 % / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RANTES

Resolution: 2.18→10 Å / Num. parameters: 4927 / Num. restraintsaints: 4188 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.299 334 5 %RANDOM
Rwork0.1857 ---
all0.1924 6225 --
obs-6019 95.8 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1231
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 0 225 1229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0208
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.086
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg3.4
X-RAY DIFFRACTIONs_plane_restr0.021
X-RAY DIFFRACTIONs_chiral_restr0.023
LS refinement shell
*PLUS
Highest resolution: 2.18 Å / Lowest resolution: 2.26 Å / Rfactor Rfree: 0.391 / Rfactor Rwork: 0.26

+
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