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- PDB-1sio: Structure of Kumamolisin-As complexed with a covalently-bound inh... -

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Basic information

Entry
Database: PDB / ID: 1sio
TitleStructure of Kumamolisin-As complexed with a covalently-bound inhibitor, AcIPF
Components
  • Ace-ILE-PRO-PHL peptide inhibitor
  • kumamolisin-As
KeywordsHYDROLASE/HYDROLASE INHIBITOR / KUMAMOLISIN-AS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


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/S53 domain superfamily / Peptidase S8/S53 domain / 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/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal / : / Kumamolisin-As
Similarity search - Component
Biological speciesAlicyclobacillus sendaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity
Authors: Wlodawer, A. / Li, M. / Gustchina, A. / Tsuruoka, N. / Ashida, M. / Minakata, H. / Oyama, H. / Oda, K. / Nishino, T. / Nakayama, T.
History
DepositionMar 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 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 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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_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

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Assembly

Deposited unit
A: kumamolisin-As
B: kumamolisin-As
C: kumamolisin-As
D: Ace-ILE-PRO-PHL peptide inhibitor
E: Ace-ILE-PRO-PHL peptide inhibitor
F: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,72612
Polymers111,3186
Non-polymers4086
Water16,844935
1
A: kumamolisin-As
D: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: kumamolisin-As
E: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-39 kcal/mol
Surface area12790 Å2
MethodPISA
3
C: kumamolisin-As
F: Ace-ILE-PRO-PHL peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2424
Polymers37,1062
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-30 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.370, 238.730, 49.250
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein kumamolisin-As


Mass: 36718.359 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 25900987, UniProt: Q8GB88*PLUS
#2: Protein/peptide Ace-ILE-PRO-PHL peptide inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 387.516 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND INHIBITOR (CHAIN D/E/F) IS ACE-ILE-PRO-PHA, N-ACETYL-L-ISOLEUCYL-L-PROLYL-L- ...THE UNBOUND INHIBITOR (CHAIN D/E/F) 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 278 OF THE ENZYME (CHAIN A/B/C) FORMING A TETRAHEDRAL HEMIACETAL. DUE TO THE CHEMICAL CHANGE, THE C-TERMINAL RESIDUE IS REPRESENTED IN SEQUENCE AS PHL, PHENYLALANINOL

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 8000, Ammonium sulfate, DTT, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9982 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2003
RadiationMonochromator: OSMIC mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99821
21.54181
ReflectionResolution: 1.8→25 Å / Num. all: 93159 / Num. obs: 93159 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.053 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rsym value: 0.311 / % possible all: 76.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GT9

1gt9


Resolution: 1.8→10 Å / Num. parameters: 34499 / Num. restraintsaints: 32199 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 4457 5.3 %RANDOM
all0.1734 89193 --
obs0.173 84178 88.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 8621
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 18 935 8621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0218
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0

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