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- PDB-6m8y: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 6m8y
TitlePSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR AIPF
Components
  • AIPF PEPTIDE INHIBITOR
  • SEDOLISIN
KeywordsHydrolase/Hydrolase inhibitor / Serine-carboxyl proteinase / Hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


sedolisin / tripeptidyl-peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family ...Peptidase S53, activation domain / Sedolisin domain / : / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal / Sedolisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsWlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / Dunn, B.M. / Oda, K.
Funding support Japan, United States, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)13460043 Japan
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK18865 & AI28571 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)intramural funds United States
CitationJournal: Biochemistry / Year: 2001
Title: Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase
Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Goldfarb, N.E. / Dunn, B.M. / Oda, K.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2018ID: 1KDY
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEDOLISIN
B: AIPF PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9197
Polymers38,5672
Non-polymers3525
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-29 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.290, 97.290, 83.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

21A-884-

HOH

DetailsAs per the authors the biological assembly is a monomer

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein SEDOLISIN / Pepstatin-insensitive carboxyl proteinase / Pseudomonapepsin / PSEUDOMONALISIN


Mass: 38179.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain 101) (bacteria)
Strain: 101 / Gene: pcp / Production host: Escherichia coli (E. coli) / References: UniProt: P42790, sedolisin
#2: Protein/peptide AIPF PEPTIDE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 387.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal

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Non-polymers , 4 types, 453 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE UNBOUND INHIBITOR (CHAIN B) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L-PHENYLALANINE ...THE UNBOUND INHIBITOR (CHAIN B) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L-PHENYLALANINE WITH C-TERMINAL PHENYLALANINAL. UPON REACTION THE INHIBITOR COVALENTLY BINDS TO THE OG ATOM OF SER A287 OF THE ENZYME FORMING A TETRAHEDRAL HEMIACETAL. DUE TO THE CHEMICAL CHANGE, THE C-TERMINAL RESIDUE IS REPRESENTED IN SEQUENCE AS PHL, PHENYLALANINOL (bound form of Phenylalaninal)

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, glycerol, guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2001 / Details: Mirrors
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.1→40 Å / Num. obs: 181161 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Χ2: 1.038 / Net I/σ(I): 14.9
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.474 / Num. unique obs: 18060 / Χ2: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHELXLrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementStarting model: 1GA6

1ga6


Resolution: 1.1→30 Å / Num. constraints: 35937 / Num. parameters: 29276 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
Details: THIS ENTRY REPRESENTS RE-REFINEMENT OF THE 1KDY DATA SET USING THE ORIGINAL DIFFRACTION DATA, CORRECTING SOME ERRORS FOUND IN THE ORIGINAL DEPOSITION
RfactorNum. reflection% reflectionSelection details
Rfree0.157 9061 5 %random
Rwork0.1322 ---
all0.1324 181109 --
obs0.1322 181109 100 %-
Displacement parametersBiso max: 131.85 Å2 / Biso mean: 15.2411 Å2 / Biso min: 5.27 Å2
Refinement stepCycle: LAST / Resolution: 1.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 20 448 3194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d1.08
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.38
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.127

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