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- PDB-1mi2: SOLUTION STRUCTURE OF MURINE MACROPHAGE INFLAMMATORY PROTEIN-2, N... -

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Basic information

Entry
Database: PDB / ID: 1mi2
TitleSOLUTION STRUCTURE OF MURINE MACROPHAGE INFLAMMATORY PROTEIN-2, NMR, 20 STRUCTURES
ComponentsMACROPHAGE INFLAMMATORY PROTEIN-2
KeywordsCYTOKINE / MIP-2 / CHEMOKINE
Function / homology
Function and homology information


Chemokine receptors bind chemokines / G alpha (i) signalling events / chemokine activity / cellular response to interleukin-1 / response to glucocorticoid / neutrophil chemotaxis / response to amphetamine / response to gamma radiation / response to molecule of bacterial origin / response to estradiol ...Chemokine receptors bind chemokines / G alpha (i) signalling events / chemokine activity / cellular response to interleukin-1 / response to glucocorticoid / neutrophil chemotaxis / response to amphetamine / response to gamma radiation / response to molecule of bacterial origin / response to estradiol / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / immune response / inflammatory response / extracellular space
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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-X-C motif chemokine 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / TORSION-ANGLE MOLECULAR DYNAMICS
AuthorsShao, W. / Jerva, L.F. / West, J. / Lolis, E. / Schweitzer, B.I.
CitationJournal: Biochemistry / Year: 1998
Title: Solution structure of murine macrophage inflammatory protein-2.
Authors: Shao, W. / Jerva, L.F. / West, J. / Lolis, E. / Schweitzer, B.I.
History
DepositionOct 24, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MACROPHAGE INFLAMMATORY PROTEIN-2
B: MACROPHAGE INFLAMMATORY PROTEIN-2


Theoretical massNumber of molelcules
Total (without water)15,7212
Polymers15,7212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein MACROPHAGE INFLAMMATORY PROTEIN-2


Mass: 7860.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P10889
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HSQC
141COSY
151ROESY

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Sample preparation

Sample conditionspH: 5.3 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: TORSION-ANGLE MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES OF THE MURINE MACROPHAGE INFLAMMATORY PROTEIN-2 (MIP-2) WERE GENERATED USING TORSION-ANGLE MOLECULAR DYNAMICS APPROACH (STEIN, E.G., RICE, L.M., & BRUNGER, A.T. (1997) J. MAGN. ...Details: THE STRUCTURES OF THE MURINE MACROPHAGE INFLAMMATORY PROTEIN-2 (MIP-2) WERE GENERATED USING TORSION-ANGLE MOLECULAR DYNAMICS APPROACH (STEIN, E.G., RICE, L.M., & BRUNGER, A.T. (1997) J. MAGN. RESON. 124, 154-164) AND X-PLOR 3.851 (ONLINE)(BRUNGER, A.T. (1992) X-PLOR (VERSION 3.1) MANUAL, YALE UNIVERSITY PRESS) BASED ON A TOTAL OF 2740 EXPERIMENTAL RESTRAINTS, COMPRISING 2596 NOE-DERIVED DISTANCE RESTRAINTS, 44 DISTANCE RESTRAINTS FOR 22 HYDROGEN BONDS, AND 100 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT MEASUREMENTS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 20

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