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- PDB-1nr4: High resolution crystal structures of thymus and activation-regul... -

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Basic information

Entry
Database: PDB / ID: 1nr4
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


CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / cellular response to type II interferon / chemotaxis ...CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / 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 / MOLECULAR REPLACEMENT / Resolution: 1.72 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 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Apr 3, 2024Group: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymus and activation-regulated chemokine
B: Thymus and activation-regulated chemokine
C: Thymus and activation-regulated chemokine
D: Thymus and activation-regulated chemokine
E: Thymus and activation-regulated chemokine
F: Thymus and activation-regulated chemokine
G: Thymus and activation-regulated chemokine
H: Thymus and activation-regulated chemokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34714
Polymers64,7708
Non-polymers5766
Water11,656647
1
A: Thymus and activation-regulated chemokine
B: Thymus and activation-regulated chemokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6737
Polymers16,1932
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-75 kcal/mol
Surface area8200 Å2
MethodPISA
2
C: Thymus and activation-regulated chemokine
D: Thymus and activation-regulated chemokine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2893
Polymers16,1932
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-30 kcal/mol
Surface area7930 Å2
MethodPISA
3
E: Thymus and activation-regulated chemokine
F: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)16,1932
Polymers16,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-25 kcal/mol
Surface area8730 Å2
MethodPISA
4
G: Thymus and activation-regulated chemokine
H: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)16,1932
Polymers16,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area8270 Å2
MethodPISA
5
A: Thymus and activation-regulated chemokine
B: Thymus and activation-regulated chemokine
hetero molecules

C: Thymus and activation-regulated chemokine
D: Thymus and activation-regulated chemokine
hetero molecules

E: Thymus and activation-regulated chemokine
F: Thymus and activation-regulated chemokine

G: Thymus and activation-regulated chemokine
H: Thymus and activation-regulated chemokine


Theoretical massNumber of molelcules
Total (without water)65,34714
Polymers64,7708
Non-polymers5766
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area12370 Å2
ΔGint-149 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.350, 56.525, 76.616
Angle α, β, γ (deg.)69.97, 85.56, 72.74
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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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.: 8 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q92583
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.16M ammonium sulfate, 0.08M Sodium acetate, 20% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 285 K / pH: 5.6 / 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

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2002 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→23 Å / Num. all: 70685 / Num. obs: 65586 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 5.1 / Num. unique all: 5781 / Rsym value: 0.26 / % possible all: 81.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 92.79 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Lowest resolution: 1.84 Å / % possible obs: 92.9 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
BEASTmodel building
AMoREphasing
EPMRphasing
DENZOdata reduction
CNSphasing
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RANTES

Resolution: 1.72→24.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.349 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23896 3316 5.1 %RANDOM
Rwork0.19917 ---
all0.2378 65586 --
obs0.20115 62269 92.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.71 Å22.03 Å2
2--0.13 Å2-0.6 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.72→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 30 647 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214314
X-RAY DIFFRACTIONr_bond_other_d0.0020.023906
X-RAY DIFFRACTIONr_angle_refined_deg2.181.975813
X-RAY DIFFRACTIONr_angle_other_deg0.9539097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155516
X-RAY DIFFRACTIONr_chiral_restr0.1310.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024693
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02896
X-RAY DIFFRACTIONr_nbd_refined0.2390.2888
X-RAY DIFFRACTIONr_nbd_other0.2520.24643
X-RAY DIFFRACTIONr_nbtor_other0.090.22721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2880.2433
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4990.289
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3750.2198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4880.270
X-RAY DIFFRACTIONr_mcbond_it1.3861.52611
X-RAY DIFFRACTIONr_mcangle_it2.47924214
X-RAY DIFFRACTIONr_scbond_it3.94731703
X-RAY DIFFRACTIONr_scangle_it6.3344.51599
LS refinement shellResolution: 1.72→1.84 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.351 553 -
Rwork0.278 10324 -
obs--85 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.029
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / Rfactor Rwork: 0.275

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