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- PDB-8vk5: Human Sputum Leucocyte Elastase (uncomplexed) -

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Basic information

Entry
Database: PDB / ID: 8vk5
TitleHuman Sputum Leucocyte Elastase (uncomplexed)
ComponentsNeutrophil elastase
KeywordsHYDROLASE / uncomplexed
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 interleukin-8 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 interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / cytokine binding / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / positive regulation of MAP kinase activity / response to UV / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / protein catabolic process / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / transcription corepressor activity / azurophil granule lumen / peptidase activity / heparin binding / protease binding / : / endopeptidase activity / response to lipopolysaccharide / 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 / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsXu, J. / Rajasekaran, G. / Li, S. / Chen, L. / Camarero, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113636 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132072 United States
CitationJournal: To Be Published
Title: Human Sputum Leucocyte Elastase (uncomplexed)
Authors: Rajasekaran, G. / Xu, J. / Li, S. / Chen, L. / Camarero, J.A.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2573
Polymers23,3191
Non-polymers9382
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.570, 73.570, 70.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11E-622-

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) / References: UniProt: P08246, leukocyte elastase
#2: 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.: 1
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
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
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.: 332 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.56→35.23 Å / Num. obs: 40278 / % possible obs: 99.95 % / Redundancy: 12.9 % / Biso Wilson estimate: 10.59 Å2 / CC1/2: 0.991 / Net I/σ(I): 12.67
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 13.1 % / Num. unique obs: 3078 / CC1/2: 0.971 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487model building
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→35.23 Å / SU ML: 0.0942 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 14.6338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1586 2005 6.5 %
Rwork0.1405 28851 -
obs0.1417 30856 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.14 Å2
Refinement stepCycle: LAST / Resolution: 1.56→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 62 332 2030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311755
X-RAY DIFFRACTIONf_angle_d1.1512392
X-RAY DIFFRACTIONf_chiral_restr0.0791289
X-RAY DIFFRACTIONf_plane_restr0.0137311
X-RAY DIFFRACTIONf_dihedral_angle_d13.2486643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.16591440.1422066X-RAY DIFFRACTION100
1.6-1.640.17091390.13712030X-RAY DIFFRACTION100
1.64-1.690.18131450.13872042X-RAY DIFFRACTION100
1.69-1.750.16751390.13832066X-RAY DIFFRACTION100
1.75-1.810.1631410.13622057X-RAY DIFFRACTION100
1.81-1.880.18551440.13282046X-RAY DIFFRACTION100
1.88-1.970.14651450.12722064X-RAY DIFFRACTION100
1.97-2.070.13441480.12862053X-RAY DIFFRACTION100
2.07-2.20.14921360.1312051X-RAY DIFFRACTION100
2.2-2.370.16311430.13012081X-RAY DIFFRACTION100
2.37-2.610.15851440.13292058X-RAY DIFFRACTION100
2.61-2.980.17191470.14932058X-RAY DIFFRACTION100
2.99-3.750.13871520.14242066X-RAY DIFFRACTION100
3.76-35.230.16711380.16022113X-RAY DIFFRACTION99.43
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)
11.2892057698-0.430916015684-0.4908760030011.310596297260.09712795280862.01551210912-0.0007257498743170.00904924881819-0.009107845604490.00537463664751-0.0170498367739-0.1868982879860.05242828492290.2084816019780.02270179676510.05774385126410.00506863118965-0.01708336093760.0480747631491-0.004267778378360.0812646017675-26.34908141270.511434403754-0.639470723622
21.83877521641-0.317286840469-0.1136813462072.73363903568-0.3642943347792.24997023508-0.0162356879349-0.3277785282920.05334606929280.1131662421240.0328390175269-0.5222968903740.2556011801890.7823388475470.1836045937310.09528694921190.0333686264768-0.05583796808220.156292783239-0.03385904866330.22259392039-17.8779468283-0.5291140516313.70769116005
32.18030716157-0.7065326316371.02061615042.112099975-0.5064212468682.23412485909-0.01629912118770.1724748667890.0205658999853-0.110394338643-0.0525009216896-0.2675566956040.04364510741590.2108297296360.06140326122710.09699159438440.01268838755020.02527271818970.0502355922796-0.02091607683340.0861858611231-26.1119889459-2.91013129087-9.3325674663
40.962227828134-0.398863646193-0.7138806763840.5722298797780.9190527253421.85885882201-0.1054135008630.213200463591-0.102008758034-0.0308931186427-0.0953486744460.1876101888630.14225974825-0.4029629743920.1855358120150.110341721565-0.0381719643377-0.003632787096370.132848567676-0.0202144616820.101121627523-44.024493397-4.36068593045-3.43194222019
52.506959345120.0566177155713-0.1620558772271.97276508643-0.3589416449591.47244512579-0.051563303268-0.03670929179330.258398773720.0871551473676-0.04829131453230.00610641812994-0.15536503892-0.1195881075720.07204517067810.07896667605110.0132513589124-0.0007003253202910.0194865425758-0.0106450082260.061513048785-38.48865601256.164882485282.53175190477
61.61675517021-0.691962300115-0.3603479349964.161700930210.5033111086073.238589512310.04040432944220.001153130133260.1889062728650.0717770669508-0.01487971067780.169347031803-0.121566308317-0.33272335124-0.03172481574510.04242523497870.00651911518092-0.01917929076320.0646267312984-0.002898615804240.0433640129457-39.19573784228.05325524034.74185447373
70.674682269361-0.0649695095022-0.3156050759280.4085687487810.5936205122382.138190434140.03314628992160.0956623223781-0.00886572823822-0.0967602736825-0.04819988054240.01883135706450.0684819832449-0.09134445188690.02244564046520.0603643496449-0.000223980251333-0.005569550638150.0474318996608-0.001213655865890.0539677003054-38.15507090070.320884641941-6.6121747004
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: E / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'E' and (resid 1 through 47 )1 - 471 - 47
22chain 'E' and (resid 48 through 67 )48 - 6748 - 67
33chain 'E' and (resid 68 through 109 )68 - 10968 - 109
44chain 'E' and (resid 110 through 126 )110 - 126110 - 126
55chain 'E' and (resid 127 through 160 )127 - 160127 - 160
66chain 'E' and (resid 161 through 175 )161 - 175161 - 175
77chain 'E' and (resid 176 through 218 )176 - 218176 - 218

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