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- PDB-1hum: SOLUTION STRUCTURE OF THE CHEMOKINE HMIP-1BETA(SLASH)ACT-2 BY MUL... -

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Entry
Database: PDB / ID: 1hum
TitleSOLUTION STRUCTURE OF THE CHEMOKINE HMIP-1BETA(SLASH)ACT-2 BY MULTI-DIMENSIONAL NMR: A NOVEL CHEMOKINE DIMER
ComponentsHUMAN MACROPHAGE INFLAMMATORY PROTEIN 1 BETA
KeywordsCYTOKINE(CHEMOTACTIC)
Function / homology
Function and homology information


CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / establishment or maintenance of cell polarity / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / cytokine activity / response to virus / response to toxic substance / cellular response to type II interferon / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / cell adhesion / immune response / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region / identical protein binding
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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Lodi, P.J. / Garrett, D.S. / Gronenborn, A.M.
CitationJournal: Science / Year: 1994
Title: High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR.
Authors: Lodi, P.J. / Garrett, D.S. / Kuszewski, J. / Tsang, M.L. / Weatherbee, J.A. / Leonard, W.J. / Gronenborn, A.M. / Clore, G.M.
History
DepositionJan 31, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN MACROPHAGE INFLAMMATORY PROTEIN 1 BETA
B: HUMAN MACROPHAGE INFLAMMATORY PROTEIN 1 BETA


Theoretical massNumber of molelcules
Total (without water)15,6492
Polymers15,6492
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein HUMAN MACROPHAGE INFLAMMATORY PROTEIN 1 BETA


Mass: 7824.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P13236
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

RefinementSoftware ordinal: 1
Details: RESTRAINED MINIMIZED AVERAGE STRUCTURE OVER 35 FILES AVE.RMS DIFF. TO MEAN FOR BACKBONE (4-69)= 0.304637 ANGSTROMS AVE.RMS DIFF. TO MEAN FOR ALL ORDERED NON-H-ATOMS (4-69)= 0.45 ANGSTROMS ...Details: RESTRAINED MINIMIZED AVERAGE STRUCTURE OVER 35 FILES AVE.RMS DIFF. TO MEAN FOR BACKBONE (4-69)= 0.304637 ANGSTROMS AVE.RMS DIFF. TO MEAN FOR ALL ORDERED NON-H-ATOMS (4-69)= 0.45 ANGSTROMS AVE.RMS DIFF. TO MEAN FOR ALL NON-H-ATOMS (4-69)= 0.706906 ANGSTROMS THE 3D STRUCTURE OF THE HMIP-1BETA DIMER IN SOLUTION BY NMR IS BASED ON 3586 EXPERIMENTAL RESTRAINTS COMPRISING: 3132 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS OF WHICH 228 ARE INTERSUBUNIT; 24 RESTRAINTS FOR 12 H-BONDS INVOLVING TIGHTLY BOUND WATER MOLECULES; 108 RESTRAINTS FOR 54 BACKBONE HYDROGEN BONDS INVOLVING SLOWLY EXCHANGING AMIDE PROTONS; 220 TORSION ANGLE RESTRAINTS (122 PHI, 10 PSI, 80 CHI1 AND 8 CHI2); AND 102 HN-HALPHA THREE-BOND COUPLING CONSTANTS. A COMPLETE LIST OF EXPERIMENTAL RESTRAINTS AND 1H, 13C AND 15N ASSIGNMENTS ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317-324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THIS ENTRY CORRESPONDS TO THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 35 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES A 4 - A 69 (CHAIN A) AND B 4 - B 69 (CHAIN B), AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE FIELD THAT CONTAINS THE B VALUE IN X-RAY STRUCTURES (COLUMNS 61 - 66) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE.
NMR ensembleConformers submitted total number: 1

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