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- PDB-3ifd: Human synthetic monocyte chemoattractant protein 1 (MCP-1) -

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Basic information

Entry
Database: PDB / ID: 3ifd
TitleHuman synthetic monocyte chemoattractant protein 1 (MCP-1)
ComponentsC-C motif chemokine 2
KeywordsCYTOKINE / chemokine / quarternary structure / peptide synthesis / Chemotaxis / Disulfide bond / Glycoprotein / Inflammatory response / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis ...helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis / cellular homeostasis / positive regulation of endothelial cell apoptotic process / NFE2L2 regulating inflammation associated genes / eosinophil chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / negative regulation of vascular endothelial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of calcium ion import / positive regulation of nitric-oxide synthase biosynthetic process / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / cell surface receptor signaling pathway via JAK-STAT / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / humoral immune response / cellular response to interleukin-1 / sensory perception of pain / cytoskeleton organization / viral genome replication / positive regulation of synaptic transmission, glutamatergic / neutrophil chemotaxis / animal organ morphogenesis / response to bacterium / cytokine-mediated signaling pathway / cellular response to type II interferon / chemotaxis / positive regulation of T cell activation / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signaling receptor binding / signal transduction / 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
: / PHOSPHATE ION / C-C motif chemokine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Biopolymers / Year: 2010
Title: Synthesis by native chemical ligation and crystal structure of human CCL2.
Authors: Grygiel, T.L. / Teplyakov, A. / Obmolova, G. / Stowell, N. / Holland, R. / Nemeth, J.F. / Pomerantz, S.C. / Kruszynski, M. / Gilliland, G.L.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: C-C motif chemokine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8333
Polymers8,6991
Non-polymers1342
Water25214
1
A: C-C motif chemokine 2
hetero molecules

A: C-C motif chemokine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6666
Polymers17,3982
Non-polymers2684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.710, 60.710, 45.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE IS A HOMODIMER.

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Components

#1: Protein C-C motif chemokine 2 / Small-inducible cytokine A2 / Monocyte chemoattractant protein 1 / Monocyte chemotactic protein 1 / ...Small-inducible cytokine A2 / Monocyte chemoattractant protein 1 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemotactic and activating factor / MCAF / Monocyte secretory protein JE / HC11


Mass: 8699.045 Da / Num. of mol.: 1 / Fragment: residues 24-99 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13500
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.78 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS PH 8.5, 2.4 M K/NA PHOSPHATE, 2% PEG 400 CRYO CONDITIONS: 0.1 M TRIS PH 8.5, 2.2 M K/NA PHOSPHATE, 2% PEG 400, 17% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 14, 2007 / Details: VARIMAX HF
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→34.4 Å / Num. obs: 6396 / % possible obs: 80.8 % / Observed criterion σ(I): -4 / Redundancy: 1.9 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.52 / % possible all: 39.7

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Processing

Software
NameVersionClassification
d*TREKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOL

1dol


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.856 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.148 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25467 294 4.6 %RANDOM
Rwork0.19264 ---
all0.19534 6079 --
obs0.19534 6079 76.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.148 Å0.141 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 6 14 547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022549
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.957741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.171565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55823.04323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19315107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.984155
X-RAY DIFFRACTIONr_chiral_restr0.0870.284
X-RAY DIFFRACTIONr_gen_planes_refined00.02391
X-RAY DIFFRACTIONr_nbd_refined0.2190.2197
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.219
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0590.21
X-RAY DIFFRACTIONr_mcbond_it2.2652333
X-RAY DIFFRACTIONr_mcangle_it3.9194546
X-RAY DIFFRACTIONr_scbond_it9.6818216
X-RAY DIFFRACTIONr_scangle_it14.30688195
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 7 -
Rwork0.336 203 -
obs--39.7 %

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