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- PDB-4mhe: Crystal structure of CC-chemokine 18 -

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Basic information

Entry
Database: PDB / ID: 4mhe
TitleCrystal structure of CC-chemokine 18
ComponentsC-C motif chemokine 18
KeywordsIMMUNE SYSTEM / Greek key shape
Function / homology
Function and homology information


CCR chemokine receptor binding / cell communication / lymphocyte chemotaxis / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / positive regulation of GTPase activity / cellular response to type II interferon ...CCR chemokine receptor binding / cell communication / lymphocyte chemotaxis / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / positive regulation of GTPase activity / cellular response to type II interferon / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / killing of cells of another organism / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space
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
ACETATE ION / C-C motif chemokine 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiang, W.G. / Tang, W.-J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.
Authors: Liang, W.G. / Ren, M. / Zhao, F. / Tang, W.J.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: C-C motif chemokine 18
B: C-C motif chemokine 18
C: C-C motif chemokine 18
D: C-C motif chemokine 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8685
Polymers31,8094
Non-polymers591
Water3,423190
1
A: C-C motif chemokine 18
D: C-C motif chemokine 18


Theoretical massNumber of molelcules
Total (without water)15,9052
Polymers15,9052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-5 kcal/mol
Surface area8540 Å2
MethodPISA
2
B: C-C motif chemokine 18
C: C-C motif chemokine 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9643
Polymers15,9052
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.075, 55.168, 60.377
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-C motif chemokine 18


Mass: 7952.254 Da / Num. of mol.: 4 / Fragment: UNP residues 21-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL18, AMAC1, DCCK1, MIP4, PARC, SCYA18 / Production host: Escherichia coli (E. coli) / References: UniProt: P55774
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 30% w/v Polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→35.033 Å / Num. all: 19084 / Num. obs: 19065 / % possible obs: 99.9 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 4 %

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2X69

2x69


Resolution: 2.1→35 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 1744 10 %
Rwork0.176 --
obs0.1803 17436 91.02 %
all-19156 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 4 190 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072146
X-RAY DIFFRACTIONf_angle_d1.0612896
X-RAY DIFFRACTIONf_dihedral_angle_d13.75823
X-RAY DIFFRACTIONf_chiral_restr0.07325
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15690.2863660.205593X-RAY DIFFRACTION42
2.1569-2.22660.27841030.1966932X-RAY DIFFRACTION65
2.2266-2.30610.25771370.1861228X-RAY DIFFRACTION86
2.3061-2.39840.23361560.19751406X-RAY DIFFRACTION98
2.3984-2.50760.25961600.2031436X-RAY DIFFRACTION100
2.5076-2.63970.27421580.20721418X-RAY DIFFRACTION100
2.6397-2.8050.27061570.20421424X-RAY DIFFRACTION100
2.805-3.02150.24631620.19941449X-RAY DIFFRACTION100
3.0215-3.32540.23221570.18761422X-RAY DIFFRACTION100
3.3254-3.80610.18721610.15151448X-RAY DIFFRACTION100
3.8061-4.79330.17581620.13871451X-RAY DIFFRACTION100
4.7933-35.03830.19221650.17371485X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 53.536 Å / Origin y: 13.3432 Å / Origin z: 18.0152 Å
111213212223313233
T0.0554 Å20.0052 Å20.0062 Å2-0.0549 Å2-0.0011 Å2--0.0438 Å2
L0.2584 °2-0.1305 °20.0633 °2-0.2242 °2-0.1284 °2--0.2285 °2
S0.037 Å °0.0232 Å °0.0246 Å °0.0227 Å °-0.0613 Å °0.0198 Å °0.0157 Å °0.0461 Å °-0.0008 Å °
Refinement TLS groupSelection details: ALL

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