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- PDB-1esr: CRYSTAL STRUCTURE OF HUMAN MONOCYTE CHEMOTACTIC PROTEIN-2 -

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Basic information

Entry
Database: PDB / ID: 1esr
TitleCRYSTAL STRUCTURE OF HUMAN MONOCYTE CHEMOTACTIC PROTEIN-2
ComponentsMONOCYTE CHEMOTACTIC PROTEIN 2
KeywordsCYTOKINE / CHEMOKINE / MONOCYTE CHEMOATTRACTANT PROTEIN / HIV-1 / PYROGLUTAMIC ACID
Function / homology
Function and homology information


negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis / response to virus ...negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / chemokine-mediated signaling pathway / eosinophil chemotaxis / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis / response to virus / intracellular calcium ion homeostasis / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / calcium ion transport / cell-cell signaling / heparin binding / protein kinase activity / positive regulation of cell migration / inflammatory response / signal transduction / extracellular space
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 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBlaszczyk, J. / Ji, X.
CitationJournal: Biochemistry / Year: 2000
Title: Complete crystal structure of monocyte chemotactic protein-2, a CC chemokine that interacts with multiple receptors.
Authors: Blaszczyk, J. / Coillie, E.V. / Proost, P. / Damme, J.V. / Opdenakker, G. / Bujacz, G.D. / Wang, J.M. / Ji, X.
History
DepositionApr 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 2.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCYTE CHEMOTACTIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)8,9111
Polymers8,9111
Non-polymers00
Water1,60389
1
A: MONOCYTE CHEMOTACTIC PROTEIN 2

A: MONOCYTE CHEMOTACTIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)17,8232
Polymers17,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)61.012, 61.012, 114.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21A-177-

HOH

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Components

#1: Protein MONOCYTE CHEMOTACTIC PROTEIN 2 / MCP-2


Mass: 8911.384 Da / Num. of mol.: 1 / Mutation: Q24(PCA) AND K69Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHEN1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80075
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.6 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
210 mMTris-HCl1drop
340 %ammonium sulfate1reservoir
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97132
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1998 / Details: Mirror
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97132 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 10447 / Num. obs: 10447 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.7854 / Num. unique all: 469 / % possible all: 92.7
Reflection
*PLUS
Num. obs: 9060 / % possible obs: 99 % / Num. measured all: 38808 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4

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Processing

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

1dok


Resolution: 2→20 Å / Num. parameters: 2793 / Num. restraintsaints: 2572 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
RfactorNum. reflection% reflectionSelection details
Rfree0.32 471 -RANDOM
Rwork0.2317 ---
obs0.244 7346 94 %-
all-8555 --
Solvent computationSolvent model: Moews & Kretsinger, J. Mol. Biol. 91 (1975) 201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 711
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 0 0 89 713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.146
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.046
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.094
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.2 Å2

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