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- PDB-6m9f: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 6m9f
TitlePSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Tyrostatin
Components
  • SEDOLISIN
  • Tyrostatin
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
TYROSTATIN (Bound Form) / Pseudomonalisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
Kitasatosporia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 23, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2018ID: 1KDZ
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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.0Jul 10, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEDOLISIN
B: Tyrostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7734
Polymers38,6372
Non-polymers1362
Water6,413356
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-28 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.240, 98.240, 83.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-819-

HOH

DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS A MONOMER

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Components

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


Mass: 38108.848 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 Tyrostatin


Type: Peptide-like / Class: Inhibitor / Mass: 527.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Kitasatosporia (bacteria) / References: TYROSTATIN (Bound Form)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND INHIBITOR (CHAIN B) IS Tyrostatin (IVA-TYR-LEU-TYB), WITH C-TERMINAL TYROSINAL. UPON ...THE UNBOUND INHIBITOR (CHAIN B) IS Tyrostatin (IVA-TYR-LEU-TYB), WITH C-TERMINAL TYROSINAL. 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 TYE, tyrosinol (bound form of TYROSINAL)

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, guanidinium hydrochloride, glycerol

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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 focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 110028 / % possible obs: 97.9 % / Redundancy: 5.32 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.546 / Num. unique obs: 11184 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SHELXL2018/3refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GA6

1ga6


Resolution: 1.3→30 Å / Num. parameters: 27940 / Num. restraintsaints: 33744 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1106 2 %RANDOM
all0.1935 ---
obs0.1932 109989 97.9 %-
Refine analyzeNum. disordered residues: 15 / Occupancy sum hydrogen: 1489 / Occupancy sum non hydrogen: 2710
Refinement stepCycle: 1 / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 25 356 3111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d1.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.36
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.138

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