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- PDB-1m8a: Human MIP-3alpha/CCL20 -

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Basic information

Entry
Database: PDB / ID: 1m8a
TitleHuman MIP-3alpha/CCL20
ComponentsSmall inducible cytokine A20
KeywordsCYTOKINE / CC-chemokine / IL-8 type dimer
Function / homology
Function and homology information


thymocyte migration / CCR6 chemokine receptor binding / chemokine activity / Chemokine receptors bind chemokines / Interleukin-10 signaling / positive regulation of T cell migration / T cell migration / cell chemotaxis / calcium-mediated signaling / chemotaxis ...thymocyte migration / CCR6 chemokine receptor binding / chemokine activity / Chemokine receptors bind chemokines / Interleukin-10 signaling / positive regulation of T cell migration / T cell migration / cell chemotaxis / calcium-mediated signaling / chemotaxis / cell-cell signaling / G alpha (i) signalling events / defense response to bacterium / immune response / inflammatory response / signal transduction / extracellular space / extracellular region
Similarity search - Function
Chemokine CC, DCCL motif-cointaining domain / 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) ...Chemokine CC, DCCL motif-cointaining domain / 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
ISOPROPYL ALCOHOL / C-C motif chemokine 20
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHoover, D.M. / Boulegue, C. / Yang, D. / Oppenheim, J.J. / Tucker, K. / Lu, W. / Lubkowski, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The structure of human macrophage inflammatory protein-3alpha /CCL20. Linking antimicrobial and CC chemokine receptor-6-binding activities with human beta-defensins
Authors: Hoover, D.M. / Boulegue, C. / Yang, D. / Oppenheim, J.J. / Tucker, K. / Lu, W. / Lubkowski, J.
History
DepositionJul 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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: Small inducible cytokine A20
B: Small inducible cytokine A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,68812
Polymers16,0872
Non-polymers60110
Water3,045169
1
A: Small inducible cytokine A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4648
Polymers8,0441
Non-polymers4217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Small inducible cytokine A20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2244
Polymers8,0441
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.822, 70.822, 71.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe molecule is likely a monomer

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Components

#1: Protein Small inducible cytokine A20 / CC-Chemokine LARC / MIP-3-alpha / CCL20 / Macrophage inflammatory protein 3 alpha / Liver and ...CC-Chemokine LARC / MIP-3-alpha / CCL20 / Macrophage inflammatory protein 3 alpha / Liver and activation-regulated chemokine / Beta chemokine exodus-1


Mass: 8043.568 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PROTEIN WAS SYNTHESIZED USING Machine-assisted stepwise solid phase peptide synthesis on an Applied Biosystems 433A synthesizer using a custom-designed program tailored from the ...Details: THE PROTEIN WAS SYNTHESIZED USING Machine-assisted stepwise solid phase peptide synthesis on an Applied Biosystems 433A synthesizer using a custom-designed program tailored from the published in situ neutralization/HBTU activation protocol for Boc chemistry (Schnolzer, M. et al. (1992) J.Pept.Protein Res. 40, 180-193). IT IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: P78556
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: isopropanol, sodium citrate, N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Temperature: 12 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1dropin water
220 %isopropanol1reservoir
3200 mMtrisodium citrate1reservoir
4100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2002 / Details: mirrors
RadiationMonochromator: si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 21953 / Num. obs: 21953 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.9 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. measured all: 99101
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 96.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EQT

1eqt


Resolution: 1.7→15 Å / Num. parameters: 4979 / Num. restraintsaints: 4435
Isotropic thermal model: anisotropic for sulfur, isotropic otherwise
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 834 4.3 %RANDOM
Rwork0.1897 ---
all0.1931 19365 --
obs0.1931 19365 97.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 27.7 Å2
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1175
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 209 1234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 4 % / Rfactor all: 0.19 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.028

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