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- PDB-1ae5: HUMAN HEPARIN BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1ae5
TitleHUMAN HEPARIN BINDING PROTEIN
ComponentsHEPARIN BINDING PROTEIN
KeywordsSERINE PROTEASE HOMOLOG / ENDOTOXIN BINDING / HEPARIN BINDING / INFLAMMATION / ANTIBACTERIAL / CAP37 / AZUROCIDIN / GLYCOSYLATED PROTEIN
Function / homologySerine proteases, trypsin domain / Peptidase S1, PA clan / Trypsin / Peptidase S1A, chymotrypsin family / Neutrophil degranulation / Serine proteases, trypsin domain profile. / neutrophil mediated killing of bacterium / monocyte activation / positive regulation of fractalkine biosynthetic process / protein kinase C signaling ...Serine proteases, trypsin domain / Peptidase S1, PA clan / Trypsin / Peptidase S1A, chymotrypsin family / Neutrophil degranulation / Serine proteases, trypsin domain profile. / neutrophil mediated killing of bacterium / monocyte activation / positive regulation of fractalkine biosynthetic process / protein kinase C signaling / cellular extravasation / glial cell migration / positive regulation of MHC class II biosynthetic process / regulation of vascular permeability / induction of positive chemotaxis / protein kinase C-activating G protein-coupled receptor signaling pathway / macrophage chemotaxis / azurophil granule membrane / positive regulation of interleukin-1 beta biosynthetic process / positive regulation of tumor necrosis factor biosynthetic process / heparan sulfate proteoglycan binding / azurophil granule / calcium-mediated signaling using intracellular calcium source / positive regulation of cell adhesion / extrinsic component of membrane / toxic substance binding / positive regulation of protein kinase activity / microglial cell activation / positive regulation of phagocytosis / antimicrobial humoral response / cell chemotaxis / positive regulation of peptidyl-threonine phosphorylation / azurophil granule lumen / defense response to virus / peptidase activity / heparin binding / defense response to Gram-negative bacterium / inflammatory response / proteolysis / positive regulation of gene expression / serine-type endopeptidase activity / neutrophil degranulation / negative regulation of apoptotic process / extracellular exosome / extracellular space / extracellular region / Azurocidin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.3 Å resolution
AuthorsIversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of HBP, a multifunctional protein with a serine proteinase fold.
Authors: Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Molecular Replacement Solution of Human Heparin Binding Protein
Authors: Iversen, L.F. / Kastrup, J.S. / Larsen, I.K. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J.
#2: Journal: FEBS Lett. / Year: 1996
Title: Characterization of Recombinant Human Hbp/CAP37/Azurocidin, a Pleiotropic Mediator of Inflammation-Enhancing Lps-Induced Cytokine Release from Monocytes
Authors: Rasmussen, P.B. / Bjorn, S. / Hastrup, S. / Nielsen, P.F. / Norris, K. / Thim, L. / Wiberg, F.C. / Flodgaard, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 5, 1997 / Release: Mar 11, 1998
RevisionDateData content typeGroupProviderType
1.0Mar 11, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPARIN BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7453
Polyers24,3021
Non-polymers4422
Water1,13563
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)39.190, 66.120, 101.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide HEPARIN BINDING PROTEIN / CAP37 / AZUROCIDIN


Mass: 24302.475 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell line: SF-900 / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Formula: H2O / Water

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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: 2.3 / Density percent sol: 46 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Iversen, L.F., (1996) Acta Crystallogr.,Sect.D, 52, 1222.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
12.5 mg/mlprotein1drop
27-10 %ethanol1drop
32.5-5 %glycerol1drop
40.05 MTris-HCl1drop
514-20 %ethanol1reservoir
65-10 %glycerol1reservoir
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 300 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE X11 / Synchrotron site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.999
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Sep 1, 1996
RadiationMonochromator: MIRRORS / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionD resolution high: 2.3 Å / D resolution low: 2 Å / Number obs: 12176 / Observed criterion sigma I: 1 / Rmerge I obs: 0.089 / Rsym value: 0.089 / NetI over sigmaI: 14.3 / Redundancy: 4.7 % / Percent possible obs: 99.2
Reflection shellRmerge I obs: 0.264 / Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / MeanI over sigI obs: 4.9 / Rsym value: 0.264 / Redundancy: 3.9 % / Percent possible all: 98.6
Reflection shell
*PLUS
Percent possible obs: 98.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPF
Details: THERE IS A DISORDERED REGION IN THE STRUCTURE INVOLVING RESIDUES 44 - 48.
Sigma F: 1
Least-squares processHighest resolution: 2.3 Å / Lowest resolution: 2 Å / Number reflection all: 12176 / Number reflection obs: 12176 / Percent reflection obs: 99.2
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 1687 / Nucleic acid: 0 / Ligand: 28 / Solvent: 63 / Total: 1778
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_dihedral_angle_d18.43
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it2.6
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.266 / R factor R work: 0.192 / R factor all: 0.192
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.43

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