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- PDB-1o7z: Crystal structure of IP-10 T-form -

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Basic information

Entry
Database: PDB / ID: 1o7z
TitleCrystal structure of IP-10 T-form
ComponentsSMALL INDUCIBLE CYTOKINE B10
KeywordsCHEMOKINE / INTERFERON INDUCTION / CHEMOTAXIS / INFLAMMATORY RESPONSE
Function / homology
Function and homology information


regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / response to auditory stimulus / CXCR chemokine receptor binding / cAMP-dependent protein kinase regulator activity / response to vitamin D / negative regulation of myoblast differentiation ...regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / response to auditory stimulus / CXCR chemokine receptor binding / cAMP-dependent protein kinase regulator activity / response to vitamin D / negative regulation of myoblast differentiation / T cell chemotaxis / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / endothelial cell activation / chemokine activity / muscle organ development / chemoattractant activity / Interleukin-10 signaling / antiviral innate immune response / positive regulation of T cell migration / negative regulation of angiogenesis / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / response to gamma radiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to virus / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to heat / heparin binding / regulation of cell population proliferation / G alpha (i) signalling events / regulation of apoptotic process / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / 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 / 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 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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-X-C motif chemokine 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSwaminathan, G.J. / Holloway, D.E. / Papageorgiou, A.C. / Acharya, K.R.
CitationJournal: Structure / Year: 2003
Title: Crystal Structures of Oligomeric Forms of the Ip-10/Cxcl10 Chemokine
Authors: Swaminathan, G.J. / Holloway, D.E. / Colvin, R.A. / Campanella, G.K. / Papageorgiou, A.C. / Luster, A.D. / Acharya, K.R.
History
DepositionNov 20, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMALL INDUCIBLE CYTOKINE B10
B: SMALL INDUCIBLE CYTOKINE B10


Theoretical massNumber of molelcules
Total (without water)17,2752
Polymers17,2752
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.437, 59.437, 121.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SMALL INDUCIBLE CYTOKINE B10 / IP-10 / CXCL10 / GAMMA-IP10 / IP-10 / INTERFERON-GAMMA INDUCED PROTEIN


Mass: 8637.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02778
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHEMOTACTIC FOR MONOCYTES AND T LYMPHOCYTES. BINDS TO CXCR3. INDUCED BY INTERFERON GAMMA. A DIVERSE ...CHEMOTACTIC FOR MONOCYTES AND T LYMPHOCYTES. BINDS TO CXCR3. INDUCED BY INTERFERON GAMMA. A DIVERSE POPULATION OF CELL TYPES RAPIDLY INCREASES TRANSCRIPTION OF MRNA ENCODING THIS PROTEIN. THIS SUGGESTS THAT GAMMA-INDUCED PROTEIN MAY BE A KEY MEDIATOR OF THE INTERFERON GAMMA RESPONSE.
Sequence detailsTHE SEQUENCE CONFLICT INDICATED IN THE SEQADV RECORDS ARISES FROM A DIFFERENCE IN THE PRIMARY ...THE SEQUENCE CONFLICT INDICATED IN THE SEQADV RECORDS ARISES FROM A DIFFERENCE IN THE PRIMARY SEQUENCE IN THE SWISS-PROT DATABASE REFERENCE P02778 AT POSITION 93. THE SEQUENCE GIVEN HERE FOLLOWS THE SEQUENCE DESCRIBED IN REFERENCE: LUSTER ET AL., NATURE, 315:672 (1985).

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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: 3.12 Å3/Da / Density % sol: 60.3 %
Crystal growpH: 8.75
Details: 10MG/ML PROTEIN,0.1M TRIS-HCL BUFFER, PH 8.75,3.3M SODIUM FORMATE
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.75
33.3 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2002 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 17435 / % possible obs: 99.8 % / Redundancy: 17.8 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.7
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.2 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 309571
Reflection shell
*PLUS
Lowest resolution: 1.99 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RHP

1rhp


Resolution: 1.92→34.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 874079.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 887 5.8 %RANDOM
Rwork0.279 ---
obs0.279 15343 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5121 Å2 / ksol: 0.35472 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.58 Å20 Å20 Å2
2--8.58 Å20 Å2
3----17.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-35 Å
Luzzati sigma a0.22 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.92→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 0 42 930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it3.392
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 1.92→1.99 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.378 67 5.1 %
Rwork0.405 1241 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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