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- PDB-1dok: MONOCYTE CHEMOATTRACTANT PROTEIN 1, P-FORM -

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Basic information

Entry
Database: PDB / ID: 1dok
TitleMONOCYTE CHEMOATTRACTANT PROTEIN 1, P-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: 1.85 Å
AuthorsLubkowski, J. / Bujacz, G. / Boque, L. / Wlodawer, A. / Domaille, P.J. / Handel, T.M.
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 27, 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: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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: MONOCYTE CHEMOATTRACTANT PROTEIN 1
B: MONOCYTE CHEMOATTRACTANT PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8534
Polymers17,6602
Non-polymers1922
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-23 kcal/mol
Surface area9190 Å2
MethodPISA
2
A: MONOCYTE CHEMOATTRACTANT PROTEIN 1
B: MONOCYTE CHEMOATTRACTANT PROTEIN 1
hetero molecules

A: MONOCYTE CHEMOATTRACTANT PROTEIN 1
B: MONOCYTE CHEMOATTRACTANT PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7058
Polymers35,3214
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6750 Å2
ΔGint-92 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.740, 50.740, 107.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.652315, -0.596164, 0.468052), (-0.546077, -0.058591, -0.835684), (0.525628, -0.800722, -0.287332)
Vector: 35.99238, 84.54701, 71.81376)

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Components

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


Mass: 8830.239 Da / Num. of mol.: 2
Mutation: N-TERMINAL METHIONINE NOT REMOVED POST-TRANSLATIONALLY
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.04 Å3/Da / Density % sol: 32 %
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: RIGAKU / Detector: IMAGE PLATE / Date: Nov 5, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→10 Å / Num. obs: 12318 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.59 % / Rsym value: 0.078 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.82 % / Mean I/σ(I) obs: 2.15 / Rsym value: 0.363 / % possible all: 94.7
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.363

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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: 1.85→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
Details: REFLECTIONS FOR R-FREE TEST SELECTED IN 10.0 - 2.0 A RESOLUTION RANGE. THE TWO CHAINS WERE REFINED INDEPENDENTLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 572 7 %RANDOM, UP TO 2.0 A
Rwork0.191 ---
obs0.191 12308 97 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 10 116 1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.191.5
X-RAY DIFFRACTIONx_mcangle_it2.322
X-RAY DIFFRACTIONx_scbond_it2.192
X-RAY DIFFRACTIONx_scangle_it2.322.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
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_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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