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- PDB-1fy3: [G175Q]HBP, A mutant of human heparin binding protein (CAP37) -

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Basic information

Entry
Database: PDB / ID: 1fy3
Title[G175Q]HBP, A mutant of human heparin binding protein (CAP37)
ComponentsHEPARIN-BINDING PROTEINAzurocidin 1
KeywordsANTIMICROBIAL PROTEIN / Serine protease homolog / BPTI binding site
Function / homology
Function and homology information


neutrophil-mediated killing of bacterium / monocyte activation / cellular extravasation / positive regulation of fractalkine production / protein kinase C signaling / glial cell migration / regulation of vascular permeability / induction of positive chemotaxis / heparan sulfate proteoglycan binding / protein kinase C-activating G protein-coupled receptor signaling pathway ...neutrophil-mediated killing of bacterium / monocyte activation / cellular extravasation / positive regulation of fractalkine production / protein kinase C signaling / glial cell migration / regulation of vascular permeability / induction of positive chemotaxis / heparan sulfate proteoglycan binding / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of MHC class II biosynthetic process / antimicrobial humoral response / azurophil granule membrane / azurophil granule / macrophage chemotaxis / : / positive regulation of cell adhesion / toxic substance binding / positive regulation of protein kinase activity / positive regulation of phagocytosis / cell chemotaxis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / microglial cell activation / azurophil granule lumen / positive regulation of tumor necrosis factor production / heparin binding / peptidase activity / defense response to virus / defense response to Gram-negative bacterium / inflammatory response / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / 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
ETHANOL / Azurocidin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsKastrup, J.S. / Linde, V. / Pedersen, A.K. / Stoffer, B. / Iversen, L.F. / Larsen, I.K. / Rasmussen, P.B. / Flodgaard, H.J. / Bjorn, S.E.
Citation
Journal: Proteins / Year: 2001
Title: Two mutants of human heparin binding protein (CAP37): toward the understanding of the nature of lipid A/LPS and BPTI binding.
Authors: Kastrup, J.S. / Linde, V. / Pedersen, A.K. / Stoffer, B. / Iversen, L.F. / Larsen, I.K. / Rasmussen, P.B. / Flodgaard, H.J. / Bjorn, S.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Atomic resolution structure of human HBP/CAP37/Azurocidin
Authors: Karlsen, S. / Iversen, L.F. / Larsen, I.K. / Flodgaard, H.J. / Kastrup, J.S.
#2: 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.
#3: 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.
#4: Journal: Protein Sci. / Year: 1999
Title: Structure and function of the N-linked glycans of HBP/CAP37/azurocidin: Crystal structure determination and biological characterization of nonglycosylated HBP
Authors: Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Wiberg, F.C. / Larsen, I.K. / Flodgaard, H.J. / Rasmussen, P.B.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEPARIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1015
Polymers24,3741
Non-polymers7274
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.003, 65.138, 100.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEPARIN-BINDING PROTEIN / Azurocidin 1 / HBP / AZUROCIDIN / CATIONIC ANTIMICROBIAL PROTEIN CAP37


Mass: 24373.553 Da / Num. of mol.: 1 / Mutation: G175Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 235 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ethanol, glycerol, TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
22-6 %ethanol1reservoir
315 %glycerol1reservoir
40.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. all: 18582 / Num. obs: 18582 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.269 / Num. unique all: 885 / % possible all: 87.7
Reflection
*PLUS
Num. measured all: 102404
Reflection shell
*PLUS
% possible obs: 87.7 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementResolution: 1.89→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.252 950 -Random
Rwork0.182 ---
all-18582 --
obs-18582 89.3 %-
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 46 233 1945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_bond_d0.009
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.2
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.011

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