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- PDB-6m9c: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 6m9c
TitlePSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Pseudotyrostatin
Components
  • Pseudotyrostatin
  • 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
PSEUDOTYROSTATIN (Bound Form) / ACETIC ACID / Sedolisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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: 1KE1
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: Pseudotyrostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15211
Polymers38,5232
Non-polymers6299
Water6,017334
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-47 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.270, 98.270, 83.300
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-721-

HOH

21A-807-

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: 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 Pseudotyrostatin


Type: Peptide-like / Class: Inhibitor / Mass: 414.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PSEUDOTYROSTATIN (Bound Form)

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Non-polymers , 4 types, 343 molecules

#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.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE UNBOUND INHIBITOR (CHAIN B) IS Pseudotyrostatin (IVA-TYR-TYB), WITH C-TERMINAL TYROSINAL. UPON ...THE UNBOUND INHIBITOR (CHAIN B) IS Pseudotyrostatin (IVA-TYR-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: 59.19 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 41476 / % possible obs: 98 % / Observed criterion σ(F): 0.046 / Redundancy: 4.95 % / Net I/σ(I): 39
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.282 / Num. unique obs: 2099 / % possible all: 99.1

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Processing

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

1ga6


Resolution: 1.8→30 Å / Num. parameters: 12379 / Num. restraintsaints: 11394 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 2060 5 %RANDOM
Rwork0.1627 ---
all0.1628 41473 --
obs0.1628 38648 98 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 2512 / Occupancy sum non hydrogen: 2721
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 36 334 3091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.35
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps

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