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- PDB-1a7s: ATOMIC RESOLUTION STRUCTURE OF HBP -

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Basic information

Entry
Database: PDB / ID: 1a7s
TitleATOMIC RESOLUTION STRUCTURE OF HBP
ComponentsHEPARIN BINDING PROTEIN
KeywordsSERINE PROTEASE HOMOLOG / ENDOTOXIN BINDING / HEPARIN
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
ETHANOL / Azurocidin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASES FROM NATIVE HBP / Resolution: 1.12 Å
AuthorsKarlsen, S. / Iversen, L.F. / Larsen, I.K. / Flodgaard, H.J. / Kastrup, J.S.
Citation
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.
#1: 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.
#2: 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.
History
DepositionMar 17, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / diffrn_source / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,67519
Polymers24,3021
Non-polymers1,37218
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.220, 65.160, 101.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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) / Strain: ACMNPV / Cell line (production host): SF-900 / Production host: Spodoptera frugiperda (fall armyworm) / 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


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, 339 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 46.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

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: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 %ethanol1reservoir
25 %1,2,6-trihydroxyhexane1reservoir
35 mM1reservoirMgSO4
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / 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: 1.12→20 Å / Num. obs: 90539 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.13
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.96 / % possible all: 81.9
Reflection shell
*PLUS
% possible obs: 81.9 % / Num. unique obs: 4055

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing
RefinementMethod to determine structure: PHASES FROM NATIVE HBP / Resolution: 1.12→15 Å / Num. parameters: 18822 / Num. restraintsaints: 85714 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Rfactor% reflectionSelection details
Rfree0.189 5 %EVERY 5TH REFLECTION
obs0.159 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1626 / Occupancy sum non hydrogen: 2083
Refinement stepCycle: LAST / Resolution: 1.12→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 88 323 2083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.13
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

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