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- PDB-1nap: THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING ... -

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Basic information

Entry
Database: PDB / ID: 1nap
TitleTHE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION
ComponentsNEUTROPHIL ACTIVATING PEPTIDE-2
KeywordsCYTOKINE
Function / homology
Function and homology information


D-glucose transmembrane transporter activity / D-glucose transmembrane transport / CXCR chemokine receptor binding / chemokine activity / Chemokine receptors bind chemokines / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide ...D-glucose transmembrane transporter activity / D-glucose transmembrane transport / CXCR chemokine receptor binding / chemokine activity / Chemokine receptors bind chemokines / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / Platelet degranulation / cellular response to lipopolysaccharide / G alpha (i) signalling events / defense response to bacterium / inflammatory response / Neutrophil degranulation / 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
Platelet basic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMalkowski, M.G. / Edwards, B.F.P.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: The crystal structure of recombinant human neutrophil-activating peptide-2 (M6L) at 1.9-A resolution.
Authors: Malkowski, M.G. / Wu, J.Y. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: The Three Dimensional Structure of Bovine Platelet Factor 4 at 3.0 Angstroms Resolution
Authors: Charles, R.St. / Walz, D.A. / Edwards, B.F.P.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal Structure of Interleukin 8: Symbiosis of NMR and Crystallography
Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.C. / Appella, E. / Yamada, M. / Matsushima, K. / Edwards, B.F.P. / Clore, G.M. / Gronenborn, A.M. / Wlodawer, A.
#3: Journal: Biochemistry / Year: 1990
Title: Three Dimensional Structure of Interleukin 8 in Solution
Authors: Clore, G.M. / Appella, E. / Yamada, M. / Matsushima, K. / Gronenborn, A.M.
History
DepositionDec 19, 1994Processing site: BNL
Revision 1.0Dec 19, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL ACTIVATING PEPTIDE-2
B: NEUTROPHIL ACTIVATING PEPTIDE-2
C: NEUTROPHIL ACTIVATING PEPTIDE-2
D: NEUTROPHIL ACTIVATING PEPTIDE-2


Theoretical massNumber of molelcules
Total (without water)30,4964
Polymers30,4964
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-34 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.770, 43.810, 44.650
Angle α, β, γ (deg.)98.37, 120.28, 92.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NEUTROPHIL ACTIVATING PEPTIDE-2 / NAP-2


Mass: 7623.935 Da / Num. of mol.: 4 / Mutation: M26L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBR-CRM-CTAP-MET20,LEU26 / Production host: Escherichia coli (E. coli) / References: UniProt: P02775
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE NUMBERING SCHEME FOR NAP-2 FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES ...THE NUMBERING SCHEME FOR NAP-2 FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES IN BOVINE PLATELET FACTOR FOUR. THE NUMBERING SCHEME IS SEQUENTIAL BEGINNING WITH RESIDUE 21 AND ENDING WITH RESIDUE 90. SEE FIGURE 1 IN THE JRNL REFERENCE LISTED ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein 1drop
228 %PEG40001reservoir
3100 mMsodium acetate1reservoir
4200 mMammonium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Num. obs: 17830 / % possible obs: 97 % / Num. measured all: 30511 / Rmerge(I) obs: 0.025
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 47 %

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Processing

Software
NameClassification
GPRLSArefinement
X-PLORrefinement
X-PLORmodel building
FRODOmodel building
X-PLORphasing
RefinementResolution: 1.9→7 Å
Details: THE MUTATION M26L IS DESCRIBED AS M6L IN THE JRNL REFERENCE.
RfactorNum. reflection
Rfree0.23 -
Rwork0.202 -
obs0.202 17475
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 0 265 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.038
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_planar_d0.041
X-RAY DIFFRACTIONx_chiral_restr0.127

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