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- PDB-9ass: Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S... -

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Basic information

Entry
Database: PDB / ID: 9ass
TitleCrystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus
Components
  • Extracellular Adherence Protein
  • Neutrophil elastase
KeywordsPROTEIN BINDING / PROTEASE INHIBITOR / IMMUNE EVASION
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of chemokine production / negative regulation of interleukin-8 production / Antimicrobial peptides / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / Activation of Matrix Metalloproteinases / cytokine binding / positive regulation of MAP kinase activity / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / positive regulation of smooth muscle cell proliferation / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / protein catabolic process / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / azurophil granule lumen / transcription corepressor activity / peptidase activity / heparin binding / : / protease binding / response to lipopolysaccharide / endopeptidase activity / defense response to bacterium / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. ...MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Neutrophil elastase / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMishra, N.B. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.
Authors: Mishra, N. / Gido, C.D. / Herdendorf, T.J. / Hammel, M. / Hura, G.L. / Fu, Z.Q. / Geisbrecht, B.V.
History
DepositionFeb 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil elastase
C: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8935
Polymers35,6552
Non-polymers1,2373
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint3 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.621, 127.383, 148.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

21A-495-

HOH

31A-522-

HOH

41C-512-

HOH

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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 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: neutrophil / References: UniProt: P08246, leukocyte elastase
#2: Protein Extracellular Adherence Protein / Protein map


Mass: 12336.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: map, SAV1938 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01 M zinc sulfate heptahydrate 0.1M MES (pH 6.5) 25% (v/v) peg-550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 44585 / % possible obs: 99.4 % / Redundancy: 10 % / CC1/2: 0.809 / CC star: 0.946 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.064 / Rrim(I) all: 0.215 / Χ2: 1.034 / Net I/σ(I): 9.3 / Num. measured all: 447621
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.75-1.815.51.5643420.580.8570.6411.6920.9497.8
1.81-1.897.21.24144390.7510.9260.4481.3221.08399.6
1.89-1.978.60.94444150.8660.9630.3230.9991.07899.8
1.97-2.079.40.75744210.1560.520.2660.8051.0799.5
2.07-2.29.50.59244170.930.9820.1980.6251.07598.7
2.2-2.3811.60.44544740.970.9920.1360.4661.056100
2.38-2.6112.10.30944660.9780.9940.0920.3231.02599.9
2.61-2.9911.90.24844620.9850.9960.0740.2591.04899.7
2.99-3.7712.10.14745180.9920.9980.0440.1541.00299.3
3.77-5012.20.10746310.9910.9980.0320.1120.96199.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→41.51 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 1984 4.47 %
Rwork0.1885 --
obs0.1896 44362 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 81 246 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072546
X-RAY DIFFRACTIONf_angle_d0.7973448
X-RAY DIFFRACTIONf_dihedral_angle_d12.413947
X-RAY DIFFRACTIONf_chiral_restr0.056417
X-RAY DIFFRACTIONf_plane_restr0.007433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.29861320.29722849X-RAY DIFFRACTION94
1.8-1.850.25471400.26522969X-RAY DIFFRACTION98
1.85-1.90.24811370.24512977X-RAY DIFFRACTION99
1.9-1.960.27211400.21853027X-RAY DIFFRACTION99
1.96-2.030.25171420.22783013X-RAY DIFFRACTION99
2.03-2.110.22661400.20132990X-RAY DIFFRACTION99
2.11-2.210.231400.19533011X-RAY DIFFRACTION98
2.21-2.330.20881430.19253045X-RAY DIFFRACTION100
2.33-2.470.20421440.18753044X-RAY DIFFRACTION100
2.47-2.660.2151430.19223056X-RAY DIFFRACTION100
2.66-2.930.21811440.19573049X-RAY DIFFRACTION100
2.93-3.350.20471430.19183051X-RAY DIFFRACTION99
3.36-4.230.18421460.16073103X-RAY DIFFRACTION100
4.23-41.510.20111500.16493194X-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)
10.09150.00280.05990.0530.07150.08530.06720.00060.0282-0.1506-0.1252-0.3248-0.099-0.0827-0.00210.23180.03780.08250.17810.03480.275511.1806-3.035-23.6706
20.1715-0.0203-0.14880.29320.37070.6230.08370.04780.1211-0.1538-0.0522-0.13750.0261-0.18640.11530.19540.03430.06850.19580.05240.20826.8022-16.6-30.8623
30.4056-0.00620.09190.42130.62460.85170.05950.0597-0.0090.03570.0711-0.34140.1247-0.01260.21490.2230.02980.05390.17130.04080.280614.5096-22.2115-28.6606
40.4039-0.0343-0.1780.0710.20370.56020.117-0.0089-0.10570.0554-0.0365-0.517-0.06020.00330.07780.1088-0.003-0.10220.17430.05240.476121.8567-13.1098-13.4437
50.0498-0.02470.02970.0354-0.0060.0180.034-0.05980.1599-0.0389-0.0232-0.02190.0338-0.0325-0.00010.19010.01630.03020.2230.02630.1843-0.2149-7.59-19.8953
60.1374-0.0608-0.17070.03570.04330.1513-0.0008-0.00160.07820.191-0.0548-0.4761-0.03410.12440.07540.25290.0262-0.11070.21230.01610.268914.857-13.9945-8.7812
70.0612-0.03640.04570.0206-0.01190.0302-0.0916-0.0582-0.04490.1227-0.0329-0.21430.08170.0329-00.19090.0139-0.03150.20090.02010.19776.2222-10.2342-12.1638
80.08830.10170.00370.4734-0.02170.16260.0983-0.0627-0.05560.4182-0.0488-0.67320.0145-0.0292-0.01030.15510.0302-0.0280.17850.03160.378616.172-18.5721-16.2305
90.2252-0.06060.17780.0224-0.04320.1683-0.26410.2260.08390.0181-0.02120.1004-0.0476-0.1252-0.12620.4607-0.29420.08090.5745-0.04360.0974-16.8388-30.0307-18.0703
100.0199-0.00270.00350.0081-0.00510.0069-0.15730.0027-0.14250.1043-0.1493-0.01770.00870.00380.00010.6865-0.15430.17910.5373-0.03750.4449-19.4711-39.5951-10.8603
110.0013-0.0022-0.00360.0181-00.006-0.02160.15460.13270.0846-0.0316-0.06680.0390.000300.417-0.2731-0.0260.70880.04960.3281-18.3933-26.0301-19.5888
12-0.0006-0.00110.00160.0049-0.0057-0.00080.05760.12510.15630.1149-0.06020.25080.0121-0.386-0.00310.1888-0.0756-0.02650.44620.08350.2417-9.5472-17.5536-23.7137
130.7875-0.4313-0.11370.25820.0660.03730.12740.13790.2685-0.0867-0.0121-0.07780.1976-0.43120.02540.2476-0.08720.00390.35230.00520.134-13.306-24.4343-10.7242
140.05640.02090.00910.0248-0.00140.0159-0.2733-0.06710.11070.04980.0171-0.11910.1359-0.1219-0.00420.317-0.07780.02650.3602-0.01130.1809-10.7769-27.56581.0828
150.0723-0.00160.00680.03220.08450.2716-0.33010.1448-0.4515-0.16230.2029-0.28320.45790.0368-0.00010.4544-0.12640.12450.2991-0.08040.1975-4.3825-32.7643-16.9803
160.04350.0563-0.01520.0589-0.04120.01980.0395-0.03850.0889-0.03650.01720.0260.305-0.19710.01730.2084-0.0365-0.00030.23450.02520.1101-0.7991-22.6267-13.2169
170.1801-0.1952-0.07060.258-0.00960.3626-0.20950.4618-0.18090.05650.1608-0.02640.23940.06150.11360.5159-0.40180.2310.53720.0333-0.1811-10.1762-32.1597-17.5807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 154 )
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 188 )
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 203 )
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 246 )
9X-RAY DIFFRACTION9chain 'C' and (resid 371 through 380 )
10X-RAY DIFFRACTION10chain 'C' and (resid 381 through 388 )
11X-RAY DIFFRACTION11chain 'C' and (resid 389 through 393 )
12X-RAY DIFFRACTION12chain 'C' and (resid 394 through 400 )
13X-RAY DIFFRACTION13chain 'C' and (resid 401 through 416 )
14X-RAY DIFFRACTION14chain 'C' and (resid 417 through 427 )
15X-RAY DIFFRACTION15chain 'C' and (resid 428 through 444 )
16X-RAY DIFFRACTION16chain 'C' and (resid 445 through 456 )
17X-RAY DIFFRACTION17chain 'C' and (resid 457 through 468 )

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