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- PDB-1dol: MONOCYTE CHEMOATTRACTANT PROTEIN 1, I-FORM -

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Basic information

Entry
Database: PDB / ID: 1dol
TitleMONOCYTE CHEMOATTRACTANT PROTEIN 1, I-FORM
ComponentsMONOCYTE CHEMOATTRACTANT PROTEIN 1
KeywordsCHEMOATTRACTANT / CYTOKINE
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
C-C motif chemokine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLubkowski, J. / Bujacz, G. / Boque, L. / Wlodawer, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions.
Authors: Lubkowski, J. / Bujacz, G. / Boque, L. / Domaille, P.J. / Handel, T.M. / Wlodawer, A.
#1: Journal: Biochemistry / Year: 1996
Title: Heteronuclear (1H, 13C, 15N) NMR Assignments and Solution Structure of the Monocyte Chemoattractant Protein-1 (Mcp-1) Dimer
Authors: Handel, T.M. / Domaille, P.J.
History
DepositionNov 22, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCYTE CHEMOATTRACTANT PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)8,8301
Polymers8,8301
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MONOCYTE CHEMOATTRACTANT PROTEIN 1

A: MONOCYTE CHEMOATTRACTANT PROTEIN 1

A: MONOCYTE CHEMOATTRACTANT PROTEIN 1

A: MONOCYTE CHEMOATTRACTANT PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)35,3214
Polymers35,3214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area6690 Å2
ΔGint-34 kcal/mol
Surface area15220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.860, 84.860, 52.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

21A-225-

HOH

31A-240-

HOH

41A-241-

HOH

51A-245-

HOH

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Components

#1: Protein MONOCYTE CHEMOATTRACTANT PROTEIN 1 / MCP-1 / MCAF


Mass: 8830.239 Da / Num. of mol.: 1 / Mutation: INS(MET0)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P13500
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE MET 0 IS AN ARTIFACT OF EXPRESSION.

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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: 2.8 Å3/Da / Density % sol: 56 %
Description: INITIAL MODEL FOR MOLECULAR REPLACEMENT WAS MODIFIED AS DESCRIBED IN JOURNAL ARTICLE.
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 10 MG/ML PROTEIN IN 50 MM TRIS BUFFER PH 7.5-8 EQUILIBRATED AGAINST 50-55% AMMONIUM SULFATE USING HANGING DROP VAPOR DIFFUSION METHOD., pH 8.0, vapor diffusion - hanging drop
PH range: 7.5-8.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMTris-HCl1drop
350-55 %(w/v)ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 11, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 3573 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 2.41 % / Rsym value: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.62 / Rsym value: 0.267 / % possible all: 82.2
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 82.2 % / Rmerge(I) obs: 0.267

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOM

1dom


Resolution: 2.4→10 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 260 7 %RANDOM
Rwork0.2 ---
obs0.2 3309 84.5 %-
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms568 0 0 52 620
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.9424
X-RAY DIFFRACTIONx_mcangle_it0.9755
X-RAY DIFFRACTIONx_scbond_it0.9424.5
X-RAY DIFFRACTIONx_scangle_it0.9755.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51

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