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- PDB-2x6l: X-ray Structure of Macrophage Inflammatory Protein-1 beta -

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Basic information

Entry
Database: PDB / ID: 2x6l
TitleX-ray Structure of Macrophage Inflammatory Protein-1 beta
ComponentsC-C MOTIF CHEMOKINE 4
KeywordsIMMUNE SYSTEM / INFLAMMATORY RESPONSE / CHEMOTAXIS
Function / homology
Function and homology information


CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / establishment or maintenance of cell polarity ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / establishment or maintenance of cell polarity / Interleukin-10 signaling / host-mediated suppression of viral transcription / positive regulation of calcium-mediated signaling / cytokine activity / response to toxic substance / response to virus / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / G alpha (i) signalling events / cell adhesion / immune response / positive regulation of cell migration / inflammatory response / signal transduction / extracellular space / extracellular region / identical protein binding
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 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.602 Å
AuthorsGuo, Q. / Ren, M. / Tang, W.
CitationJournal: Embo J. / Year: 2010
Title: Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme.
Authors: Ren, M. / Guo, Q. / Guo, L. / Lenz, M. / Qian, F. / Koenen, R.R. / Xu, H. / Schilling, A.B. / Weber, C. / Ye, R.D. / Dinner, A.R. / Tang, W.
History
DepositionFeb 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
SupersessionApr 6, 2011ID: 3KKH
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 4
B: C-C MOTIF CHEMOKINE 4
C: C-C MOTIF CHEMOKINE 4
D: C-C MOTIF CHEMOKINE 4
E: C-C MOTIF CHEMOKINE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4008
Polymers39,1245
Non-polymers2763
Water2,612145
1
A: C-C MOTIF CHEMOKINE 4
B: C-C MOTIF CHEMOKINE 4
C: C-C MOTIF CHEMOKINE 4
D: C-C MOTIF CHEMOKINE 4
E: C-C MOTIF CHEMOKINE 4
hetero molecules

A: C-C MOTIF CHEMOKINE 4
B: C-C MOTIF CHEMOKINE 4
C: C-C MOTIF CHEMOKINE 4
D: C-C MOTIF CHEMOKINE 4
E: C-C MOTIF CHEMOKINE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,80016
Polymers78,24710
Non-polymers5536
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area18030 Å2
ΔGint-70.9 kcal/mol
Surface area31060 Å2
MethodPISA
2
C: C-C MOTIF CHEMOKINE 4
E: C-C MOTIF CHEMOKINE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7423
Polymers15,6492
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-11.4 kcal/mol
Surface area8310 Å2
MethodPISA
3
B: C-C MOTIF CHEMOKINE 4
D: C-C MOTIF CHEMOKINE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8344
Polymers15,6492
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10.1 kcal/mol
Surface area8150 Å2
MethodPISA
4
A: C-C MOTIF CHEMOKINE 4

A: C-C MOTIF CHEMOKINE 4


Theoretical massNumber of molelcules
Total (without water)15,6492
Polymers15,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1590 Å2
ΔGint-11.5 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.811, 87.892, 186.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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Components

#1: Protein
C-C MOTIF CHEMOKINE 4 / SMALL-INDUCIBLE CYTOKINE A4 / MACROPHAGE INFLAMMATORY PROTEIN 1-BETA / MIP-1-BETA(1-69) / T-CELL ...SMALL-INDUCIBLE CYTOKINE A4 / MACROPHAGE INFLAMMATORY PROTEIN 1-BETA / MIP-1-BETA(1-69) / T-CELL ACTIVATION PROTEIN 2 / PAT 744 / PROTEIN H400 / SIS-GAMMA / LYMPHOCYTE ACTIVATION GENE 1 PROTEIN / HC21 / G-26 T-LYMPHOCYTE-SECRETED PROTEIN / MIP-1-BETA(3-69) / MIP-1-BETA / ACT-2 / LAG-1 / MACROPHAGE INFLAMMATORY PROTEIN-1 BETA


Mass: 7824.742 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13236
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15529 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.602→49.448 Å / SU ML: 0.31 / σ(F): 0.16 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 738 5 %
Rwork0.1864 --
obs0.1899 14811 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.241 Å2 / ksol: 0.405 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.7341 Å2-0 Å2-0 Å2
2---5.494 Å20 Å2
3----4.2402 Å2
Refinement stepCycle: LAST / Resolution: 2.602→49.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 18 145 2790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082747
X-RAY DIFFRACTIONf_angle_d1.0453732
X-RAY DIFFRACTIONf_dihedral_angle_d21.849987
X-RAY DIFFRACTIONf_chiral_restr0.071403
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6016-2.80250.26261380.1932614X-RAY DIFFRACTION90
2.8025-3.08440.29211390.19772699X-RAY DIFFRACTION93
3.0844-3.53070.27081660.18052821X-RAY DIFFRACTION96
3.5307-4.44780.25391340.16422918X-RAY DIFFRACTION98
4.4478-49.45660.23441610.19173021X-RAY DIFFRACTION98

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