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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 / homology
Function and homology information


monocyte activation / monocyte extravasation / neutrophil-mediated killing of bacterium / cellular extravasation / positive regulation of fractalkine production / glial cell migration / induction of positive chemotaxis / regulation of vascular permeability / antimicrobial humoral response / positive regulation of MHC class II biosynthetic process ...monocyte activation / monocyte extravasation / neutrophil-mediated killing of bacterium / cellular extravasation / positive regulation of fractalkine production / glial cell migration / induction of positive chemotaxis / regulation of vascular permeability / antimicrobial humoral response / positive regulation of MHC class II biosynthetic process / heparan sulfate proteoglycan binding / azurophil granule / azurophil granule membrane / macrophage chemotaxis / toxic substance binding / positive regulation of phagocytosis / positive regulation of cell adhesion / protein maturation / positive regulation of interleukin-1 beta production / cell chemotaxis / microglial cell activation / positive regulation of tumor necrosis factor production / azurophil granule lumen / peptidase activity / heparin binding / defense response to Gram-negative bacterium / phospholipase C-activating G protein-coupled receptor signaling pathway / defense response to virus / intracellular signal transduction / inflammatory response / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
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.
History
DepositionMar 5, 1997Processing site: BNL
Revision 1.0Mar 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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
Polymers24,3021
Non-polymers4422
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP212121

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Components

#1: Protein HEPARIN BINDING PROTEIN / CAP37 / AZUROCIDIN


Mass: 24302.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF-900 / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % 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
IDConc.Common 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 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12176 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.264 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPF

1ppf


Resolution: 2.3→20 Å / σ(F): 1
Details: THERE IS A DISORDERED REGION IN THE STRUCTURE INVOLVING RESIDUES 44 - 48.
Num. reflection% reflection
all12176 -
obs12176 99.2 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 28 63 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
Refinement
*PLUS
Rfactor all: 0.192 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.43

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