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- PDB-4nzl: Extracellular proteins of Staphylococcus aureus inhibit the neutr... -

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Basic information

Entry
Database: PDB / ID: 4nzl
TitleExtracellular proteins of Staphylococcus aureus inhibit the neutrophil serine proteases
Components
  • Neutrophil elastase
  • Uncharacterized protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Primarily beta / Serine protease / protease inhibitor / innate immunity / Azurophilic granules / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / 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 ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / 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 / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / peptidase activity / heparin binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / cytoplasm / cytosol
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / Ubiquitin-like (UB roll) / 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. ...MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / Ubiquitin-like (UB roll) / 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 / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MAP domain-containing protein / Neutrophil elastase / MAP domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStapels, D.A.C. / von Koeckritz-Blickwede, M. / Ramyar, K.X. / Bischoff, M. / Milder, F. / Ruyken, M. / Scheepmaker, L. / McWhorter, W.J. / Herrmann, M. / van Kessel, K.P.M. ...Stapels, D.A.C. / von Koeckritz-Blickwede, M. / Ramyar, K.X. / Bischoff, M. / Milder, F. / Ruyken, M. / Scheepmaker, L. / McWhorter, W.J. / Herrmann, M. / van Kessel, K.P.M. / Geisbrecht, B.V. / Rooijakkers, S.H.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Staphylococcus aureus secretes a unique class of neutrophil serine protease inhibitors.
Authors: Stapels, D.A. / Ramyar, K.X. / Bischoff, M. / von Kockritz-Blickwede, M. / Milder, F.J. / Ruyken, M. / Eisenbeis, J. / McWhorter, W.J. / Herrmann, M. / van Kessel, K.P. / Geisbrecht, B.V. / Rooijakkers, S.H.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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: Neutrophil elastase
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5074
Polymers36,0412
Non-polymers1,4652
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint4 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.952, 94.952, 84.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 23318.982 Da / Num. of mol.: 1 / Fragment: mature neutrophil elastase / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase
#2: Protein Uncharacterized protein


Mass: 12722.285 Da / Num. of mol.: 1 / Fragment: unp residues 43-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV2205 / Plasmid: pT7HMT EapH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99S64, UniProt: A0A0H3K0M1*PLUS
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 298 K / pH: 7
Details: 1.0 M succinic acid, 0.1 M Na-HEPES, 1% (w/v) PEG 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2207
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2012 / Details: VERTICAL FOCUSING MIRRORS
RadiationMonochromator: SI (111) ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2207 Å / Relative weight: 1
ReflectionResolution: 1.85→47.48 Å / Num. obs: 366006 / % possible obs: 100 % / Observed criterion σ(I): 4.1 / Redundancy: 9.9 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 25.9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: dev_1525)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q76 AND 1YN4

3q76

1yn4


Resolution: 1.85→47.476 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 1776 4.98 %
Rwork0.166 --
obs0.1681 35647 96.77 %
all-36833 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→47.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 98 291 2785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072551
X-RAY DIFFRACTIONf_angle_d1.1093470
X-RAY DIFFRACTIONf_dihedral_angle_d11.805889
X-RAY DIFFRACTIONf_chiral_restr0.059429
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.90010.25051280.20392469X-RAY DIFFRACTION91
1.9001-1.9560.22321330.18212470X-RAY DIFFRACTION93
1.956-2.01920.20721340.17592533X-RAY DIFFRACTION95
2.0192-2.09130.2261340.1662522X-RAY DIFFRACTION94
2.0913-2.17510.1971300.17062567X-RAY DIFFRACTION96
2.1751-2.27410.2511320.16822601X-RAY DIFFRACTION96
2.2741-2.3940.19951390.17122612X-RAY DIFFRACTION97
2.394-2.54390.19581380.16932629X-RAY DIFFRACTION98
2.5439-2.74030.21381380.17592648X-RAY DIFFRACTION98
2.7403-3.01610.20421450.18642685X-RAY DIFFRACTION99
3.0161-3.45240.22051420.17612679X-RAY DIFFRACTION100
3.4524-4.34920.20141440.14722706X-RAY DIFFRACTION100
4.3492-47.49160.18651390.14862750X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67230.37310.03280.94930.25221.06710.04820.0430.01070.051-0.0232-0.03960.04640.09580.00130.1355-0.0087-0.00180.13220.01570.1365-33.140120.5559-1.7211
20.1552-0.042-0.01310.1692-0.00240.3574-0.2533-0.07470.3976-0.25430.01860.1654-0.8293-0.2364-0.16590.54020.0711-0.11830.2368-0.04660.3535-39.015846.2224-1.6731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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