[English] 日本語
Yorodumi
- PDB-5xwj: Crystal Structure of Porcine pancreatic trypsin with tripeptide i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xwj
TitleCrystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, TRE, at pH 7
Components
  • Acetylated-THR-ARG-GLU Inhibitor
  • Trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Biological speciesSus scrofa (pig)
Capsicum annuum (sweet pepper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaikhedkar, N.S. / Bhoite, A.S. / Giri, A.P. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
CSIRBSC0120 India
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2018
Title: Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera.
Authors: Saikhedkar, N.S. / Joshi, R.S. / Bhoite, A.S. / Mohandasan, R. / Yadav, A.K. / Fernandes, M. / Kulkarni, K.A. / Giri, A.P.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trypsin
C: Acetylated-THR-ARG-GLU Inhibitor
B: Trypsin
D: Acetylated-THR-ARG-GLU Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9187
Polymers49,7204
Non-polymers1983
Water7,981443
1
A: Trypsin
C: Acetylated-THR-ARG-GLU Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0184
Polymers24,8602
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-21 kcal/mol
Surface area9080 Å2
MethodPISA
2
B: Trypsin
D: Acetylated-THR-ARG-GLU Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9003
Polymers24,8602
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-13 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.435, 101.311, 116.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Trypsin / Porcine pancreatic trypsin


Mass: 24428.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Commercially available trypsin from Sigma (Cat. no. T4799)
Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin
#2: Protein/peptide Acetylated-THR-ARG-GLU Inhibitor


Mass: 431.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Capsicum annuum (sweet pepper)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 70% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.89 Å / Num. obs: 67984 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6707 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOQ

4doq


Resolution: 1.8→42.286 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.1
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 3366 4.95 %RANDOM
Rwork0.162 ---
obs0.163 67953 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 10 443 3773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083412
X-RAY DIFFRACTIONf_angle_d0.9584644
X-RAY DIFFRACTIONf_dihedral_angle_d6.9472724
X-RAY DIFFRACTIONf_chiral_restr0.065521
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82570.30511300.29212668X-RAY DIFFRACTION99
1.8257-1.8530.29811490.25762636X-RAY DIFFRACTION100
1.853-1.88190.26191250.24332699X-RAY DIFFRACTION100
1.8819-1.91280.23221350.22952675X-RAY DIFFRACTION100
1.9128-1.94580.20251230.2112650X-RAY DIFFRACTION100
1.9458-1.98120.22371350.20442695X-RAY DIFFRACTION100
1.9812-2.01930.22581430.19782631X-RAY DIFFRACTION100
2.0193-2.06050.21161310.18242677X-RAY DIFFRACTION100
2.0605-2.10530.22071390.1762668X-RAY DIFFRACTION100
2.1053-2.15430.19271530.17232667X-RAY DIFFRACTION100
2.1543-2.20810.19951160.17282711X-RAY DIFFRACTION100
2.2081-2.26780.21461420.16392658X-RAY DIFFRACTION100
2.2678-2.33460.18431300.15092684X-RAY DIFFRACTION100
2.3346-2.40990.15761560.152665X-RAY DIFFRACTION100
2.4099-2.4960.17931550.15262661X-RAY DIFFRACTION100
2.496-2.59590.1881460.14992685X-RAY DIFFRACTION100
2.5959-2.71410.14181370.15552684X-RAY DIFFRACTION100
2.7141-2.85710.21521500.15672694X-RAY DIFFRACTION100
2.8571-3.03610.16621450.15472696X-RAY DIFFRACTION100
3.0361-3.27040.17071440.14442712X-RAY DIFFRACTION100
3.2704-3.59940.17121410.13612732X-RAY DIFFRACTION100
3.5994-4.11990.14621530.12812713X-RAY DIFFRACTION100
4.1199-5.18910.13921310.13542790X-RAY DIFFRACTION100
5.1891-42.2980.1971570.19352836X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.13290.0280.13830.8138-0.28391.1337-0.02430.12210.266-0.04090.01630.0284-0.11370.02180.00670.1378-0.0071-0.00320.1280.00690.14397.944-13.8044-3.4407
22.03050.36950.77532.21161.68713.6980.033-0.1470.00180.19710.1681-0.28510.25770.4508-0.11080.20450.0189-0.01230.2527-0.07610.216931.3308-6.798925.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:231)
2X-RAY DIFFRACTION2(chain B and resseq 9:231)

+
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