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- PDB-6m9d: PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 6m9d
TitlePSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Chymostatin
Components
  • Chymostatin A
  • 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
Chymostatin A (bound form) / Sedolisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: 1KE2
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: Chymostatin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7593
Polymers38,7192
Non-polymers401
Water3,963220
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-18 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.570, 98.570, 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-607-

HOH

21A-608-

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 Chymostatin A


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 609.717 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The first residue (PHE) of the inhibitor chymostatin A was not visible in the electron density map and is not modeled in the structure
Source: (synth.) synthetic construct (others) / References: Chymostatin A (bound form)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND INHIBITOR (CHAIN B) IS Chymostatin A (PHE-CSI-LEU-PHA), WITH C-TERMINAL PHENYLALANINAL. ...THE UNBOUND INHIBITOR (CHAIN B) IS Chymostatin A (PHE-CSI-LEU-PHA), 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: 3.02 Å3/Da / Density % sol: 59.28 %
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: Jun 11, 2001 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 28260 / % possible obs: 92.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1.012 / Net I/av σ(I): 16.7 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.033.350.39614420.883193
2.03-2.070.33714140.946193.4
2.07-2.110.29513970.988194
2.11-2.150.28414350.93193.9
2.15-2.20.25714270.97194.1
2.2-2.250.22914551.02194.8
2.25-2.310.19814301.011194.8
2.31-2.370.18514510.976194.9
2.37-2.440.16314451.036194.1
2.44-2.520.14714171.02193.5
2.52-2.610.13114471.021194.3
2.61-2.710.11414311.045194.1
2.71-2.840.10113861.083192.6
2.84-2.990.08314261.092191.6
2.99-3.170.06613841.122191.1
3.17-3.420.05413960.959191.5
3.42-3.760.04413920.917189.8
3.76-4.310.03613741.166189.7
4.31-5.420.03213681.137188.2
5.42-300.03113430.853185.1

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Processing

Software
NameVersionClassification
SHELX2018/3refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GA6

1ga6


Resolution: 2→30 Å / Num. parameters: 11771 / Num. restraintsaints: 11294 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1409 5 %RANDOM
Rwork0.1883 ---
all0.1886 28258 --
obs0.1883 26053 92.4 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2529 / Occupancy sum non hydrogen: 2722
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 1 220 2943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.317
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps

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