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- PDB-1fuj: PR3 (MYELOBLASTIN) -

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Basic information

Entry
Database: PDB / ID: 1fuj
TitlePR3 (MYELOBLASTIN)
ComponentsPR3
KeywordsHYDROLASE (SERINE PROTEASE) / HYDROLASE / SERINE PROTEASE / GLYCOPROTEIN / ZYMOGEN
Function / homology
Function and homology information


myeloblastin / mature conventional dendritic cell differentiation / cell-cell junction maintenance / neutrophil degranulation / neutrophil extravasation / antimicrobial humoral response / negative regulation of phagocytosis / Antimicrobial peptides / Other interleukin signaling / plasma membrane raft ...myeloblastin / mature conventional dendritic cell differentiation / cell-cell junction maintenance / neutrophil degranulation / neutrophil extravasation / antimicrobial humoral response / negative regulation of phagocytosis / Antimicrobial peptides / Other interleukin signaling / plasma membrane raft / membrane protein ectodomain proteolysis / collagen catabolic process / phagocytosis / Common Pathway of Fibrin Clot Formation / serine-type peptidase activity / positive regulation of GTPase activity / cytokine-mediated signaling pathway / azurophil granule lumen / blood coagulation / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / Neutrophil degranulation / enzyme binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Resolution: 2.2 Å
AuthorsFujinaga, M. / Chernaia, M.M. / Halenbeck, R. / Koths, K. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of PR3, a neutrophil serine proteinase antigen of Wegener's granulomatosis antibodies.
Authors: Fujinaga, M. / Chernaia, M.M. / Halenbeck, R. / Koths, K. / James, M.N.
#1: Journal: Embo J. / Year: 1986
Title: X-Ray Crystal Structure of the Complex of Human Leukocyte Elastase (Pmn Elastase) and the Third Domain of the Turkey Ovomucoid Inhibitor
Authors: Bode, W. / Wei, A.Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S.
History
DepositionJan 25, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: 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 / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR3
B: PR3
C: PR3
D: PR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6138
Polymers97,1434
Non-polymers1,4694
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.603, 54.070, 113.506
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PR3 / MYELOBLASTIN


Mass: 24285.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: BACULOVIRUS / Production host: unidentified baculovirus / References: UniProt: P24158
#2: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING IS ACCORDING TO ALIGNMENT WITH CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
20.5 mMCTAB1drop
343 %sat1reservoir(NH4)2SO4
4100 mMBis-Tris propane1reservoir
52 %MPD1reservoir
1protein1drop0.002ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.98→68.7 Å / Num. obs: 65602 / % possible obs: 90 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 191704 / Rmerge(I) obs: 0.073

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(F): 0 /
Num. reflection% reflection
obs49712 93.4 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 96 246 7174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011
X-RAY DIFFRACTIONt_gen_planes0.015
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d1
X-RAY DIFFRACTIONt_angle_deg1
X-RAY DIFFRACTIONt_planar_d20.011
X-RAY DIFFRACTIONt_plane_restr50.015

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