[English] 日本語
Yorodumi
- PDB-3uou: Crystal structure of the Kunitz-type protease inhibitor ShPI-1 Ly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uou
TitleCrystal structure of the Kunitz-type protease inhibitor ShPI-1 Lys13Leu mutant in complex with pancreatic elastase
Components
  • Chymotrypsin-like elastase family member 1
  • Kunitz-type proteinase inhibitor SHPI-1
KeywordsHYDROLASE/Hydrolase Inhibitor / PROTEIN-PROTEIN INTERACTION / HYDROLASE (SERINE PROTEASE) / KUNITZ-TYPE INHIBITOR / HYDROLASE-Hydrolase Inhibitor complex
Function / homology
Function and homology information


nematocyst / pancreatic elastase / aspartic-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin-like elastase family member 1 / PI-stichotoxin-She2a
Similarity search - Component
Biological speciesStichodactyla helianthus (sea anemone)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia-Fernandez, R. / Perbandt, M. / Rehders, D. / Gonzalez-Gonzalez, Y. / Chavez, M.A. / Betzel, C. / Redecke, L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Three-dimensional Structure of a Kunitz-type Inhibitor in Complex with an Elastase-like Enzyme.
Authors: Garcia-Fernandez, R. / Perbandt, M. / Rehders, D. / Ziegelmuller, P. / Piganeau, N. / Hahn, U. / Betzel, C. / Chavez, M.A. / Redecke, L.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
B: Kunitz-type proteinase inhibitor SHPI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,45117
Polymers32,0382
Non-polymers1,41315
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-135 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.750, 47.180, 42.680
Angle α, β, γ (deg.)90.00, 100.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

-
Components

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1


Mass: 25929.016 Da / Num. of mol.: 1 / Fragment: Peptidase S1 domain / Source method: isolated from a natural source / Details: Pancreas / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Protein Kunitz-type proteinase inhibitor SHPI-1


Mass: 6108.968 Da / Num. of mol.: 1 / Fragment: Kunitz-type proteinase inhibitor SHPI-1 / Mutation: K13L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / Plasmid: pPICZalphaC / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P31713
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.425M ammonium sulfate, 0.085M tri-sodium citrate, 0.85M Lithium sulfate, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2→29.647 Å / Num. obs: 17481 / % possible obs: 96.8 % / Observed criterion σ(I): 6.2 / Redundancy: 4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2→2.1239 Å / % possible all: 80.3

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNJ, PDB ENTRY 3OFW

1qnj

3ofw


Resolution: 2→29.647 Å / SU ML: 0.52 / σ(F): 1.43 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 892 5.1 %Random
Rwork0.1657 ---
obs0.168 17474 98.07 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.139 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4863 Å20 Å24.6244 Å2
2--13.2011 Å20 Å2
3----1.4417 Å2
Refinement stepCycle: LAST / Resolution: 2→29.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 82 206 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072444
X-RAY DIFFRACTIONf_angle_deg1.0473336
X-RAY DIFFRACTIONf_dihedral_angle_d13.321861
X-RAY DIFFRACTIONf_chiral_restr0.072366
X-RAY DIFFRACTIONf_plane_restr0.004423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12390.26921370.20722568X-RAY DIFFRACTION91
2.1239-2.28790.24951500.1822746X-RAY DIFFRACTION99
2.2879-2.5180.25171570.17652795X-RAY DIFFRACTION99
2.518-2.88210.23091330.16812790X-RAY DIFFRACTION100
2.8821-3.63010.18841430.16142824X-RAY DIFFRACTION100
3.6301-29.65010.17671720.14742859X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -19.125 Å / Origin y: 3.2727 Å / Origin z: 9.9495 Å
111213212223313233
T0.0615 Å20.0159 Å20.0004 Å2-0.0698 Å20.0185 Å2--0.0617 Å2
L0.8243 °20.0305 °2-0.152 °2-0.6213 °2-0.0027 °2--1.0128 °2
S0.0567 Å °0.1055 Å °0.0248 Å °-0.0476 Å °0.0202 Å °-0.0042 Å °-0.0946 Å °-0.0007 Å °-0.0321 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 266
2X-RAY DIFFRACTION1allB1 - 54
3X-RAY DIFFRACTION1allA1 - 436
4X-RAY DIFFRACTION1allA - B1 - 57
5X-RAY DIFFRACTION1allB - A1 - 271

+
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