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- PDB-1o7y: Crystal structure of IP-10 M-form -

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Basic information

Entry
Database: PDB / ID: 1o7y
TitleCrystal structure of IP-10 M-form
ComponentsSMALL INDUCIBLE CYTOKINE B10
KeywordsCHEMOKINE / INTERFERON INDUCTION / CHEMOTAXIS / INFLAMMATORY RESPONSE
Function / homology
Function and homology information


regulation of T cell chemotaxis / CXCR3 chemokine receptor binding / negative regulation of myoblast fusion / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / T cell chemotaxis / negative regulation of myoblast differentiation ...regulation of T cell chemotaxis / CXCR3 chemokine receptor binding / negative regulation of myoblast fusion / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / T cell chemotaxis / negative regulation of myoblast differentiation / response to vitamin D / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / endothelial cell activation / chemokine activity / blood circulation / muscle organ development / chemoattractant activity / Interleukin-10 signaling / positive regulation of T cell migration / antiviral innate immune response / neutrophil chemotaxis / negative regulation of angiogenesis / 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 / heparin binding / regulation of cell population proliferation / cellular response to heat / G alpha (i) signalling events / cellular response to lipopolysaccharide / regulation of apoptotic process / 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: 3 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: SMALL INDUCIBLE CYTOKINE B10
D: SMALL INDUCIBLE CYTOKINE B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7426
Polymers34,5494
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.979, 53.722, 53.366
Angle α, β, γ (deg.)90.00, 105.72, 90.00
Int Tables number5
Space group name H-MC121

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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.: 4 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02778
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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.
Has protein modificationY
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: 2.77 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 4.4
Details: 10MG/ML PROTEIN, 16% PEG 4000, 0.1M SODIUM ACETATE BUFFER, PH 4.4, 0.2M AMMONIUM SULPHATE
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1dropin water
20.1 Msodium acetate1reservoirpH4.4
316 %PEG40001reservoir
40.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 4, 1998 / Details: MIRRORS
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 7390 / % possible obs: 95.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.6 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 57731
Reflection shell
*PLUS
% possible obs: 92.8 %

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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: 3→19.93 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1063324.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 472 6.4 %RANDOM
Rwork0.267 ---
obs0.267 7367 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.239968 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1--21.65 Å20 Å2-15.14 Å2
2--2.95 Å20 Å2
3---18.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.48 Å
Luzzati d res low-20 Å
Luzzati sigma a0.7 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 10 0 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.091 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.596 43 6.1 %
Rwork0.389 663 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 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_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.61

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