[English] 日本語
Yorodumi
- PDB-2r3z: Crystal structure of mouse IP-10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r3z
TitleCrystal structure of mouse IP-10
ComponentsSmall-inducible cytokine B10
KeywordsATTRACTANT / IP-10/CXCL10 / chemokine / chemotaxis / inflammatory response
Function / homology
Function and homology information


regulation of T cell chemotaxis / Chemokine receptors bind chemokines / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / G alpha (i) signalling events / CXCR chemokine receptor binding / negative regulation of myoblast differentiation / T cell chemotaxis / chemokine-mediated signaling pathway ...regulation of T cell chemotaxis / Chemokine receptors bind chemokines / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / G alpha (i) signalling events / CXCR chemokine receptor binding / negative regulation of myoblast differentiation / T cell chemotaxis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / leukocyte chemotaxis / chemokine activity / endothelial cell activation / positive regulation of leukocyte chemotaxis / chemoattractant activity / positive regulation of T cell migration / negative regulation of angiogenesis / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / response to bacterium / adenylate cyclase-activating G protein-coupled receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / heparin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / regulation of apoptotic process / defense response to virus / killing of cells of another organism / positive regulation of cell migration / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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) ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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-X-C motif chemokine 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJabeen, T. / Leonard, P. / Jamaluddin, H. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of mouse IP-10, a chemokine
Authors: Jabeen, T. / Leonard, P. / Jamaluddin, H. / Acharya, K.R.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small-inducible cytokine B10
B: Small-inducible cytokine B10
C: Small-inducible cytokine B10
D: Small-inducible cytokine B10


Theoretical massNumber of molelcules
Total (without water)30,7014
Polymers30,7014
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-24 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.957, 71.530, 39.577
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit of the structure contains two biological units in the form of two dimers

-
Components

#1: Protein
Small-inducible cytokine B10 / CXCL-10 chemokine / CXCL10 / Interferon-gamma-induced protein CRG-2 / Gamma-IP10 / IP-10 / C7


Mass: 7675.205 Da / Num. of mol.: 4 / Fragment: residues 23-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cxcl10, Crg2, Ifi10, Inp10, Scyb10 / Production host: Escherichia coli (E. coli) / References: UniProt: P17515
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 0.2M CaCl2, 35% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2004 / Details: mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si 111SINGLE WAVELENGTHMx-ray1
2si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 9824 / Num. obs: 9824 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.0696
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.26 / Num. unique all: 725 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7Y

1o7y


Resolution: 2.5→19.79 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 386160.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3082 507 5.3 %RANDOM
Rwork0.2753 ---
all0.2754 ---
obs0.2754 9481 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.7046 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.99 Å20 Å2-12.64 Å2
2---8.71 Å20 Å2
3---16.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 81 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.472 72 5.1 %
Rwork0.37 1342 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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://pdbjlvh1.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