[English] 日本語
Yorodumi
- PDB-3qtl: Structural Basis for Dual-inhibition Mechanism of a Non-classical... -

+
Open data


ID or keywords:

Loading...

-
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 / proteolysis / extracellular space
Similarity search - Function
Kazal-type serine protease inhibitor domain / 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 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Kazal-type serine protease inhibitor domain / 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 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / 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 / Serine proteases, subtilase domain profile. / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more