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- PDB-1nlu: Pseudomonas sedolisin (serine-carboxyl proteinase) complexed with... -

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Basic information

Entry
Database: PDB / ID: 1nlu
TitlePseudomonas sedolisin (serine-carboxyl proteinase) complexed with two molecules of pseudo-iodotyrostatin
Components
  • PSEUDO-IODOTYROSTATIN
  • SEDOLISIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PSCP / 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
PSEUDO-IODOTYROSTATIN / Sedolisin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.3 Å
AuthorsWlodawer, A. / Li, M. / Gustchina, A. / Dauter, Z. / Uchida, K. / Oyama, H. / Glodfarb, N.E. / Dunn, B.M. / Oda, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Two inhibitor molecules bound in the active site of Pseudomonas sedolisin: a model for the bi-product complex following cleavage of a peptide substrate.
Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Oyama, H. / Oda, K. / Beyer, B.B. / Clemente, J. / Dunn, B.M.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEDOLISIN
B: PSEUDO-IODOTYROSTATIN
C: PSEUDO-IODOTYROSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3364
Polymers39,2963
Non-polymers401
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-26 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.840, 97.840, 82.680
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-573-

HOH

21A-695-

HOH

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Components

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


Mass: 38250.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: PCP / Production host: Escherichia coli (E. coli) / References: UniProt: P42790, sedolisin
#2: Protein/peptide PSEUDO-IODOTYROSTATIN


Type: Peptide-like / Class: Inhibitor / Mass: 522.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE INHIBITOR WAS CHEMICALLY SYNTHESIZED. / References: PSEUDO-IODOTYROSTATIN
#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.: 484 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 4.8 / Method: unknown / Details: Wlodawer, A., (2001) Biochemistry, 40, 15602.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlenzyme1drop
30.1 M1dropNaCl
45 mM1dropCaCl2
55 %guanidine hydrochloride1reservoir
610 %glycerol1reservoir
75 %methanol1reservoir
844-50 %ammonium sulfate1reservoir
90.1 Msodium acetate1reservoirpH4.3
2sodium acetate1droppH4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 110018 / Num. obs: 110018 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rsym value: 0.082 / Net I/σ(I): 20.3
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 2.28 / Num. unique all: 10917 / Rsym value: 0.77 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 848476 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.3→10 Å / Num. parameters: 28486 / Num. restraintsaints: 34716 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 5501 -RANDOM
Rwork0.164 ---
all-109765 --
obs-109756 94.9 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3137
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 1 484 3237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.092
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Rfactor Rfree: 0.1944 / Rfactor Rwork: 0.1637
Solvent computation
*PLUS
Displacement parameters
*PLUS

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