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- PDB-5ltl: Structure of human chemokine CCL16 -

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Basic information

Entry
Database: PDB / ID: 5ltl
TitleStructure of human chemokine CCL16
ComponentsC-C motif chemokine 16Chemokine
KeywordsCYTOKINE / Chemokine / CC-type / Chemotaxis
Function / homology
Function and homology information


CCR chemokine receptor binding / cell communication / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / chemoattractant activity / monocyte chemotaxis / cellular response to interleukin-1 ...CCR chemokine receptor binding / cell communication / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / chemoattractant 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 / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / 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 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWeiergraeber, O.H. / Batra-Safferling, R. / Haenel, K. / Willbold, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: To Be Published
Title: Structure and dynamics of human chemokine CCL16
Authors: Weiergraeber, O.H. / Petrovic, D. / Kislat, A. / Pattky, M. / Fabig, J. / Batra-Safferling, R. / Haenel, K. / Huhn, C. / Strodel, B. / Homey, B. / Willbold, D.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C motif chemokine 16
B: C-C motif chemokine 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0324
Polymers22,9172
Non-polymers1152
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-21 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.350, 24.590, 37.970
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C-C motif chemokine 16 / Chemokine / Chemokine CC-4 / HCC-4 / Chemokine LEC / IL-10-inducible chemokine / LCC-1 / Liver-expressed ...Chemokine CC-4 / HCC-4 / Chemokine LEC / IL-10-inducible chemokine / LCC-1 / Liver-expressed chemokine / Lymphocyte and monocyte chemoattractant / LMC / Monotactin-1 / MTN-1 / NCC-4 / Small-inducible cytokine A16


Mass: 11458.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL16, ILINCK, NCC4, SCYA16 / Plasmid: pET-15b / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): SHuffle T7 / References: UniProt: O15467
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M sodium phosphate, 0.5 M sodium chloride, 10 % (v/v) glycerol, 1.6 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2013
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→37.91 Å / Num. obs: 22666 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.6
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.883 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8T

2q8t


Resolution: 1.45→37.91 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.1976 1134 5 %
Rwork0.1705 --
obs0.1719 22637 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 7 90 1172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061185
X-RAY DIFFRACTIONf_angle_d1.0491629
X-RAY DIFFRACTIONf_dihedral_angle_d11.296447
X-RAY DIFFRACTIONf_chiral_restr0.074185
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.51590.25411400.26262644X-RAY DIFFRACTION99
1.5159-1.59580.26831390.22192630X-RAY DIFFRACTION99
1.5958-1.69580.20261390.20152641X-RAY DIFFRACTION99
1.6958-1.82670.26651430.18242704X-RAY DIFFRACTION100
1.8267-2.01050.20411400.17622661X-RAY DIFFRACTION99
2.0105-2.30140.21571420.16722707X-RAY DIFFRACTION100
2.3014-2.89940.20261420.18712700X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.79670.8621-1.34713.2877-1.23643.9855-0.02980.1574-0.0255-0.25110.0545-0.02150.0552-0.0597-0.02430.161-0.0164-0.00790.1586-0.03170.15168.676311.782410.8319
23.1650.203-0.67243.52430.77144.9473-0.0636-0.1708-0.01130.13480.1263-0.0794-0.13390.273-0.05650.1446-0.0051-0.02120.2211-0.02730.177823.080415.9653-11.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 8:75
2X-RAY DIFFRACTION2chain B and resid 8:76

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