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- PDB-1gtl: The thermostable serine-carboxyl type proteinase, kumamolisin (KS... -

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Basic information

Entry
Database: PDB / ID: 1gtl
TitleThe thermostable serine-carboxyl type proteinase, kumamolisin (KSCP) - complex with Ac-Ile-Pro-Phe-cho
Components
  • ALDEHYDE INHIBITOR
  • KUMAMOLYSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE-CARBOXYL TYPE PROTEINASE / THERMOSTABLE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


kumamolysin / tripeptidyl-peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / 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 / Subtilase family / Peptidase S8/S53 domain ...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 / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal / Kumamolisin
Similarity search - Component
Biological speciesBACILLUS NOVOSP. MN-32 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsComellas-Bigler, M. / Fuentes-Prior, P. / Maskos, K. / Huber, R. / Oyama, H. / Uchida, K. / Dunn, B.M. / Oda, K. / Bode, W.
CitationJournal: Structure / Year: 2002
Title: The 1.4 A Crystal Structure of Kumamolysin. A Thermostable Serine-Carboxyl-Type Proteinase
Authors: Comellas-Bigler, M. / Fuentes-Prior, P. / Maskos, K. / Huber, R. / Oyama, H. / Uchida, K. / Dunn, B.M. / Oda, K. / Bode, W.
History
DepositionJan 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 21, 2016Group: Source and taxonomy / Structure summary
Revision 1.4Feb 28, 2018Group: Advisory / Data collection
Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / 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_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: KUMAMOLYSIN
2: KUMAMOLYSIN
3: ALDEHYDE INHIBITOR
4: ALDEHYDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6818
Polymers73,4094
Non-polymers2724
Water3,801211
1
1: KUMAMOLYSIN
3: ALDEHYDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8414
Polymers36,7052
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-29 kcal/mol
Surface area13110 Å2
MethodPISA
2
2: KUMAMOLYSIN
4: ALDEHYDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8414
Polymers36,7052
Non-polymers1362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-29 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.030, 78.300, 73.170
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KUMAMOLYSIN


Mass: 36317.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS NOVOSP. MN-32 (bacteria)
Description: BACTERIUM FOUND IN HOTSPRING WATER NEAR VOLCANOES
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 109 / References: UniProt: Q8RR56*PLUS
#2: Protein/peptide ALDEHYDE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 387.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND INHIBITOR (CHAIN 3/4) IS ACE-ILE-PRO-PHA, N-ACETYL-L- ISOLEUCYL-L-PROLYL-L- ...THE UNBOUND INHIBITOR (CHAIN 3/4) 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 1/2) 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growpH: 4.5 / Details: PH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→24.91 Å / Num. obs: 13434 / % possible obs: 89.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.4 / % possible all: 89.6
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 26276
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 89.6 %

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GA1

1ga1


Resolution: 2.8→12 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 -4.6 %RANDOM
Rwork0.197 ---
obs0.197 13563 90.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 12 211 5407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 12 Å / Num. reflection obs: 12871 / Rfactor obs: 0.214 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS

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