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- PDB-2z7f: Crystal structure of the complex of human neutrophil elastase wit... -

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Basic information

Entry
Database: PDB / ID: 2z7f
TitleCrystal structure of the complex of human neutrophil elastase with 1/2SLPI
Components
  • Antileukoproteinase
  • Leukocyte elastase
KeywordsHydrolase/Hydrolase inhibitor / serine protease / serine protease inhibitor / Disease mutation / Glycoprotein / Hydrolase / Zymogen / Secreted / Hydrolase-Hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


modulation of process of another organism / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production ...modulation of process of another organism / leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / negative regulation of viral genome replication / endopeptidase inhibitor activity / Activation of Matrix Metalloproteinases / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / cytokine binding / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / phagocytic vesicle / response to UV / transcription repressor complex / Degradation of the extracellular matrix / secretory granule / negative regulation of protein binding / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / serine-type endopeptidase inhibitor activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / positive regulation of immune response / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / response to lipopolysaccharide / defense response to bacterium / immune response / serine-type endopeptidase activity / innate immune response / mRNA binding / Neutrophil degranulation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / cell surface / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
: / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / : / Few Secondary Structures ...: / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / : / Few Secondary Structures / Irregular / 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 family, serine active site. / 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
Antileukoproteinase / Neutrophil elastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTakimoto-Kamimura, M. / Fukushima, K.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2008
Title: Complex of human neutrophil elastase with 1/2SLPI
Authors: Koizumi, M. / Fujino, A. / Fukushima, K. / Kamimura, T. / Takimoto-Kamimura, M.
History
DepositionAug 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_special_symmetry / struct_asym / struct_conn / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 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
E: Leukocyte elastase
I: Antileukoproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5764
Polymers28,8422
Non-polymers7352
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint2 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.638, 106.638, 55.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11E-361-

HOH

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Components

#1: Protein Leukocyte elastase / Elastase-2 / Neutrophil elastase / PMN elastase / Bone marrow serine protease / Medullasin / Human ...Elastase-2 / Neutrophil elastase / PMN elastase / Bone marrow serine protease / Medullasin / Human leukocyte elastase / HLE


Mass: 23318.982 Da / Num. of mol.: 1 / Fragment: Peptidase S1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: sputum / Production host: Escherichia coli (E. coli) / References: UniProt: P08246, leukocyte elastase
#2: Protein/peptide Antileukoproteinase / ALP / Secretory leukocyte protease inhibitor / HUSI-1 / Seminal proteinase inhibitor / BLPI / Mucus ...ALP / Secretory leukocyte protease inhibitor / HUSI-1 / Seminal proteinase inhibitor / BLPI / Mucus proteinase inhibitor / MPI / WAP four-disulfide core domain protein 4 / Protease inhibitor WAP4


Mass: 5522.736 Da / Num. of mol.: 1 / Fragment: WAP 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P03973
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Na-Acetate, 2.0M Na-Formate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.32 Å / Num. obs: 35374 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.84 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.5
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 11.96 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 134 / % possible all: 99.61

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREP(CCP4 6.01 suite)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.761 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23062 1770 5 %RANDOM
Rwork0.20285 ---
obs0.20422 33575 99.45 %-
all-35374 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 48 249 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.982863
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48122.44286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91315332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4951522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2905
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.51365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33622123
X-RAY DIFFRACTIONr_scbond_it1.9673824
X-RAY DIFFRACTIONr_scangle_it3.1324.5740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 134 -
Rwork0.206 2438 -
obs--99.61 %

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