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- PDB-1qnk: TRUNCATED HUMAN GROB[5-73], NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1qnk
TitleTRUNCATED HUMAN GROB[5-73], NMR, 20 STRUCTURES
ComponentsC-X-C motif chemokine 2
KeywordsCHEMOKINE / CHEMOKINE 15-O / HUMAN CHEMOKINE GROB[5-73] / CXC CHEMOKINE
Function / homology
Function and homology information


CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / neutrophil chemotaxis / response to molecule of bacterial origin / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / G alpha (i) signalling events ...CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / neutrophil chemotaxis / response to molecule of bacterial origin / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / G alpha (i) signalling events / cellular response to lipopolysaccharide / inflammatory response / extracellular space / extracellular region
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQian, Y.Q. / Johanson, K. / McDevitt, P.
Citation
Journal: J. Mol. Biol. / Year: 1999
Title: Nuclear magnetic resonance solution structure of truncated human GRObeta [5-73] and its structural comparison with CXC chemokine family members GROalpha and IL-8.
Authors: Qian, Y.Q. / Johanson, K.O. / McDevitt, P.
#1: Journal: Blood / Year: 1995
Title: Characterization and Purification of a Stromal Cell Derived Hematopoietic Synergistic Factor Induced by a Novel Hematoregulatory Compound, Sk&F 107647
Authors: King, A. / Scott, R. / Wu, D. / Strickler, J. / Mcnulty, D. / Scott, M.
History
DepositionOct 18, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-X-C motif chemokine 2
B: C-X-C motif chemokine 2


Theoretical massNumber of molelcules
Total (without water)15,1062
Polymers15,1062
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 / 80target function
Representative

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Components

#1: Protein C-X-C motif chemokine 2 / Growth-regulated protein beta / Gro-beta / Macrophage inflammatory protein 2-alpha / MIP2-alpha


Mass: 7553.010 Da / Num. of mol.: 2 / Fragment: Residues 5-73
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: BLOOD / Gene: CXCL2, GRO2, GROB, MIP2A, SCYB2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): (LW 14) / References: UniProt: P19875

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D
NMR detailsText: SEE JRNL ARTICLE FOR DETAILS THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, TORSION ANGLE DYNAMICS AND RESTRAINED ENERGY ...Text: SEE JRNL ARTICLE FOR DETAILS THREE-DIMENSIONAL STRUCTURE IN AQUEOUS SOLUTION REPRESENTED BY 20 CONFORMERS DETERMINED BY NUCLEAR MAGNETIC RESONANCE, TORSION ANGLE DYNAMICS AND RESTRAINED ENERGY REFINEMENT. DATA WERE COLLECTED AT 30 DEGREES CELSIUS AND AT PH 5.5. THEY CONSIST OF 1878 UPPER LIMITS ON DISTANCES OBTAINED FROM NOE MEASUREMENTS AND 314 ANGLE CONSTRAINTS OBTAINED FROM NOE MEASUREMENTS AND COUPLING CONSTANT MEASUREMENTS. THERE INPUT DATA ARE ALSO AVAILABLE FROM THE PROTEIN DATA BANK. TORSION ANGLE DYNAMICS CALCULATIONS WERE PERFORMED WITH THE PROGRAM DYANA (P.GUNTERT, C.MUMENTHALER, K.WUTHRICH, J.MOL.BIOL. (1997) VOL. 273, 283-298).

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Sample preparation

DetailsContents: 90%H2O/10%D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / 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

NMR software
NameVersionDeveloperClassification
PROGRAM FOR NMR OR THEORETICAL MODELING MODELINGMODELINGJONES,ZOU,COWAN,KJELDGAARDrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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