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- PDB-1tvx: NEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITI... -

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Basic information

Entry
Database: PDB / ID: 1tvx
TitleNEUTROPHIL ACTIVATING PEPTIDE-2 VARIANT FORM M6L WITH FIVE ADDITIONAL AMINO TERMINAL RESIDUES (DSDLY)
ComponentsNEUTROPHIL ACTIVATING PEPTIDE 2 VARIANT
KeywordsCYTOKINE
Function / homology
Function and homology information


glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity ...glucose transmembrane transporter activity / glucose transmembrane transport / CXCR chemokine receptor binding / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / positive regulation of cell division / neutrophil chemotaxis / platelet alpha granule lumen / growth factor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / Platelet degranulation / tertiary granule lumen / G alpha (i) signalling events / cellular response to lipopolysaccharide / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMalkowski, M.G. / Edwards, B.F.P.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence.
Authors: Malkowski, M.G. / Lazar, J.B. / Johnson, P.H. / Edwards, B.F.
#1: 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.
#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. / Clore, G.M. / Gronenborn, A.M. / al., et
#3: Journal: J.Biol.Chem. / Year: 1989
Title: The Three-Dimensional Structure of Bovine Platelet Factor 4 at 3.0-A Resolution
Authors: Charles, R.St. / Walz, D.A. / Edwards, B.F.
History
DepositionNov 5, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL ...SHEET THERE IS A TETRAMER IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR IDENTICAL MONOMERS. TWO MONOMERS COMBINE TO FORM AN EXTENDED SIX STRANDED BETA SHEET DIMER. TWO DIMERS ARE THEN ARRANGED BACK-TO-BACK TO FORM THE TETRAMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8704
Polymers32,8704
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-31 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.810, 76.760, 43.780
Angle α, β, γ (deg.)90.00, 96.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 8217.521 Da / Num. of mol.: 4
Mutation: M26L AND A FIVE RESIDUE (DSDLY) INSERT AT THE AMINO TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02775
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUMBERING SCHEME FOR ASP-CTAP FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE ...THE NUMBERING SCHEME FOR ASP-CTAP FOLLOWS HOMOLOGY ALIGNMENT WITH THE FIRST PAIR OF CYSTEINE RESIDUES IN BOVINE PLATELET FACTOR FOUR. THE NUMBERING SCHEME IS SEQUENTIAL BEGINNING WITH RESIDUE 16 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growpH: 7.5 / Details: 1.6M CITRATE, 0.1M HEPES, PH 7.5
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 Msodium citrate1reservoir
20.1 MHEPES1reservoir
310 mg/mlprotein1drop
410 mM1drop(NH4)2PO4

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→9.6 Å / Num. obs: 25385 / % possible obs: 88 % / Observed criterion σ(I): 1 / Rsym value: 0.0388
Reflection
*PLUS
Num. measured all: 50642 / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NEUTROPHIL ACTIVATING PEPTIDE-2 (1NAP)

1nap


Resolution: 1.75→7 Å
RfactorNum. reflection
Rfree0.251 -
Rwork0.196 -
obs0.196 25118
Refinement stepCycle: LAST / Resolution: 1.75→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 0 147 2207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.06
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.34
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.85
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 21058
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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