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- PDB-6th7: Structure of porcine pancreatic elastase in complex with tutuilamide -

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Basic information

Entry
Database: PDB / ID: 6th7
TitleStructure of porcine pancreatic elastase in complex with tutuilamide
Components
  • (Tutuilamide) x 2
  • Chymotrypsin-like elastase family member 1
KeywordsHYDROLASE / elastase / inhibitor
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO4116_3_1 Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Tutuilamides A-C: Vinyl-Chloride-Containing Cyclodepsipeptides from Marine Cyanobacteria with Potent Elastase Inhibitory Properties.
Authors: Keller, L. / Canuto, K.M. / Liu, C. / Suzuki, B.M. / Almaliti, J. / Sikandar, A. / Naman, C.B. / Glukhov, E. / Luo, D. / Duggan, B.M. / Luesch, H. / Koehnke, J. / O'Donoghue, A.J. / Gerwick, W.H.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Dec 28, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_caveat / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_caveat.text / _entity_src_nat.common_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
B: Chymotrypsin-like elastase family member 1
C: Tutuilamide
D: Tutuilamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8976
Polymers53,8174
Non-polymers802
Water5,044280
1
A: Chymotrypsin-like elastase family member 1
C: Tutuilamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9493
Polymers26,9092
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chymotrypsin-like elastase family member 1
D: Tutuilamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9493
Polymers26,9092
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.258, 99.114, 117.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1


Mass: 25929.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide Tutuilamide


Mass: 979.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Protein/peptide Tutuilamide


Mass: 979.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (synth.) Synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0sodium acetate, tri-sodium citrate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→75.64 Å / Num. obs: 36608 / % possible obs: 99.01 % / Redundancy: 4.3 % / Biso Wilson estimate: 30.04 Å2 / Rmerge(I) obs: 0.1015 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.32 Å / Num. unique obs: 5124 / CC1/2: 0.507

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVY

1lvy


Resolution: 2.2→36.3 Å / SU ML: 0.2884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 1784 4.88 %
Rwork0.2003 34742 -
obs0.2025 36526 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 146 280 4069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773873
X-RAY DIFFRACTIONf_angle_d1.08925298
X-RAY DIFFRACTIONf_chiral_restr0.0593598
X-RAY DIFFRACTIONf_plane_restr0.0051681
X-RAY DIFFRACTIONf_dihedral_angle_d8.01112161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.37421130.32282536X-RAY DIFFRACTION95.84
2.26-2.330.36531320.29732609X-RAY DIFFRACTION98.21
2.33-2.40.33921230.28542641X-RAY DIFFRACTION99.35
2.4-2.490.33431240.26022693X-RAY DIFFRACTION99.93
2.49-2.590.29641250.24842682X-RAY DIFFRACTION99.89
2.59-2.70.28551500.23992643X-RAY DIFFRACTION99.86
2.7-2.850.25761470.22592674X-RAY DIFFRACTION99.61
2.85-3.020.23161310.22012658X-RAY DIFFRACTION99.57
3.02-3.260.28731410.21282696X-RAY DIFFRACTION99.58
3.26-3.590.26441290.17782704X-RAY DIFFRACTION99.68
3.59-4.10.20171400.15482696X-RAY DIFFRACTION98.99
4.1-5.170.17511460.13482708X-RAY DIFFRACTION98.45
5.17-36.30.19781830.18392802X-RAY DIFFRACTION98.55
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)
13.069544363190.2583431201012.728820746092.96026335431-0.1727976415022.518644818450.104197740877-0.0589597436828-0.1004189599270.244866186364-0.09339849822910.2122898865490.185186807541-0.1648619603160.008376681596140.159267542895-0.05514284495040.07251971953480.2364513900560.005571328150810.17474100833-17.627059910311.8597537082.29856789218
26.845318942443.8314423339-4.563450212345.20527773733-2.837382152613.225271744320.141984520011-0.1475553524550.4563399406050.4690298238470.266353413879-0.0281194259066-0.354825113420.117802928684-0.3395359490570.2347849205810.104625587989-0.06570312631140.320332146622-0.03487632915240.237996636158-13.049954682220.97021464276.63666466995
31.806114777810.4307889010180.4468156046551.08439985330.06720932156531.537352221960.06855013091270.0905074246027-0.1117520251150.05418822768390.0726919507878-0.04466866433790.1471161922640.0569543024962-0.1279572000010.1390658317810.04017882146550.002056068719120.189360003623-0.005813165132890.174617443589-11.614872261212.4054151585-0.756526096205
43.334165680624.14715089084-2.145296660418.51528941393-2.91684158746.585598508220.468263080837-0.03957982860770.1534180229110.0778077007122-0.01276027987910.752363564134-0.0423729087925-0.850857367932-0.2498319725010.0871765649280.08746309399920.02612951367640.227014566845-0.03812593264670.172994319198-28.546729001418.4351840046-3.56700112529
51.86100081299-0.06615625323910.2020914134852.31041455670.01103760377842.902976462860.04463024484670.3530538994660.0525873584538-0.184220503847-0.00564775503691-0.02242346884380.06442284830320.104764543556-0.03582901387810.1696867164130.00932302788007-0.01114308923980.291051031130.008670577306330.165042249839-14.466299169116.5275514732-15.2715577727
64.03049773737-4.075621446963.376526969124.97920145587-4.621843888537.634938474560.1080683604110.4310352237130.0884646732506-0.0261101127215-0.223774449788-0.151117745794-0.0297698954280.584996156060.1122627116920.133175299604-0.06626341686440.02930939671420.143167656502-0.0419767096670.162766288729-8.8077411772818.9204339615-9.0950356502
74.237526076080.7368445576260.8140554099095.49959617629-0.4281905667564.711612271070.0286809573523-0.00475559785829-0.6403129416080.01257704538040.0164590095741-0.6467185277950.3906524376040.54304064176-0.07974437546880.2090542438790.0521295030771-0.007025235176240.3006584681730.01896580617260.303552204727-14.0831188044-20.2479532691-27.0888650206
83.79876745380.7673069484140.09683092594193.46222511278-0.2516682028663.57709889128-0.02730258485550.0908351820637-0.4744101933990.16831983232-0.14817331088-0.4721771722280.5576410187890.4131615904440.1874338256640.3239278331760.07169672330480.00676468880860.3205805594240.008573648118530.270648568998-16.9684461851-22.2015899231-23.8581714878
95.939081383590.02896672794611.684024127827.307816307530.9407919644070.9308721771140.291089910877-0.357134923950.6226599290250.326176838096-0.2870416942840.416834791911-0.353472197623-0.163241581590.03251203546180.2939140811310.0105020914465-0.04290284217320.372048605295-0.08104825112950.176611015212-24.8331808939-5.19240452983-17.486552757
103.21798975457-0.215474217892-0.09463113977492.35069125605-0.3075281211533.6673879916-0.0453612675579-0.060541713510.1958073838920.129311875075-0.0633859940564-0.189082146895-0.325626338390.2284587956540.09949210002050.240775520753-0.0339957640974-0.03216069904940.263160551603-0.05629936517470.183284441532-20.3818546405-4.0155820263-30.4429046508
112.41023672864-0.163362364933-0.7093659145463.50239097328-0.9143853957573.102213774410.09607023153010.05807934165410.1071715590850.262347036909-0.1516068515140.0299898813188-0.213768603895-0.1978475533310.0510070207070.3210769753960.00246139743341-0.04990278755260.298517605487-0.0919824244970.215655539927-25.4620726863-5.96338064796-29.643640133
122.23576476795-0.0619294586684-1.354182133863.01303241923-0.09530623875330.87144364164-0.11690775734-0.4533820659030.1772423333670.3937577602410.0384891259455-0.317340985823-0.5498489912030.41696665070.1722826094770.33322379087-0.00725240846895-0.04817786178850.378577623113-0.06373262067920.2501684869-21.8339503659-8.43443903827-18.0427646457
132.187133983391.83021624184-1.370111753936.32483975673-3.743126684515.60122228964-0.015168879126-0.266607951922-0.03048195058830.215721748606-0.140241956690.02732297241560.168054536337-0.2523799261420.1150164456420.230101100132-0.0263677861869-0.008783441854430.412185901428-0.07035069420420.180043875529-27.5621090092-13.1907750369-25.5668215399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 266 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 83 )
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 157 )
10X-RAY DIFFRACTION10chain 'B' and (resid 158 through 190 )
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 216 )
12X-RAY DIFFRACTION12chain 'B' and (resid 217 through 234 )
13X-RAY DIFFRACTION13chain 'B' and (resid 235 through 266 )

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