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- PDB-3qtl: Structural Basis for Dual-inhibition Mechanism of a Non-classical... -

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Basic information

Entry
Database: PDB / ID: 3qtl
TitleStructural Basis for Dual-inhibition Mechanism of a Non-classical Kazal-type Serine Protease Inhibitor from Horseshoe Crab in Complex with Subtilisin
Components
  • Kazal-type serine protease inhibitor SPI-1
  • Subtilisin-like serin protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE -KAZAL TYPE SERINE PROTEASE INHIBITOR COMPLEX / HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


serine-type endopeptidase activity / metal ion binding
Similarity search - Function
Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Subtilisin Carlsberg-like catalytic domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Subtilisin Carlsberg-like catalytic domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kazal-type serine protease inhibitor SPI-1 / Keratinase / Alkaline protease
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
Carcinoscorpius rotundicauda (Southeast Asian horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsShenoy, R.T. / Sivaraman, J.
CitationJournal: Plos One / Year: 2011
Title: Structural basis for dual-inhibition mechanism of a non-classical kazal-type serine protease inhibitor from horseshoe crab in complex with subtilisin.
Authors: Shenoy, R.T. / Thangamani, S. / Velazquez-Campoy, A. / Ho, B. / Ding, J.L. / Sivaraman, J.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin-like serin protease
B: Subtilisin-like serin protease
C: Subtilisin-like serin protease
D: Kazal-type serine protease inhibitor SPI-1


Theoretical massNumber of molelcules
Total (without water)90,2304
Polymers90,2304
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Subtilisin-like serin protease
C: Subtilisin-like serin protease
D: Kazal-type serine protease inhibitor SPI-1


Theoretical massNumber of molelcules
Total (without water)62,9243
Polymers62,9243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area21400 Å2
MethodPISA
3
B: Subtilisin-like serin protease


Theoretical massNumber of molelcules
Total (without water)27,3061
Polymers27,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.840, 65.072, 111.909
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Subtilisin-like serin protease


Mass: 27306.199 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 106-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: aprE / Production host: Escherichia coli (E. coli)
References: UniProt: Q1EM64, UniProt: Q6PNN5*PLUS, subtilisin
#2: Protein Kazal-type serine protease inhibitor SPI-1


Mass: 8311.360 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carcinoscorpius rotundicauda (Southeast Asian horseshoe crab)
Gene: SPI-1 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A1X1V8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% (w/v) PEG 20000, 0.1M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.5418 Å
DetectorDate: Sep 29, 2007
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 32884 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.3 % / Rsym value: 0.34 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
PHENIX1.6_289refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCA

1sca


Resolution: 2.6→14.901 Å / SU ML: 0.36 / σ(F): 0.14 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1973 6.08 %RANDOM
Rwork0.1994 ---
obs0.2036 32432 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 44.037 Å2 / ksol: 0.431 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.3136 Å2-0 Å2-0.1614 Å2
2---2.6434 Å2-0 Å2
3---10.957 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6244 0 0 157 6401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046356
X-RAY DIFFRACTIONf_angle_d0.828666
X-RAY DIFFRACTIONf_dihedral_angle_d15.8462094
X-RAY DIFFRACTIONf_chiral_restr0.0551012
X-RAY DIFFRACTIONf_plane_restr0.0031144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.69240.28691950.2034299399
2.6924-2.79960.2941930.1931300299
2.7996-2.92610.27631960.1959301199
2.9261-3.07910.26741980.1946304199
3.0791-3.27010.26651960.2006302199
3.2701-3.51950.2641960.1978304499
3.5195-3.8680.28181980.19313052100
3.868-4.4150.25031980.1883068100
4.415-5.51510.27131990.20473085100
5.5151-14.90110.23852040.19793142100

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