[English] 日本語
Yorodumi
- PDB-2xtt: Bovine trypsin in complex with evolutionary enhanced Schistocerca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xtt
TitleBovine trypsin in complex with evolutionary enhanced Schistocerca gregaria protease inhibitor 1 (SGPI-1-P02)
Components
  • CATIONIC TRYPSIN
  • PROTEASE INHIBITOR SGPI-1
KeywordsHYDROLASE / CATALYTIC MECHANISM / INHIBITION / IN VITRO EVOLUTION
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / : / 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. ...Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / : / 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 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
ACETATE ION / Serine protease inhibitor I/II / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
SCHISTOCERCA GREGARIA (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsWahlgren, W.Y. / Pal, G. / Kardos, J. / Porrogi, P. / Szenthe, B. / Patthy, A. / Graf, L. / Katona, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.
Authors: Wahlgren, W.Y. / Pal, G. / Kardos, J. / Porrogi, P. / Szenthe, B. / Patthy, A. / Graf, L. / Katona, G.
History
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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.pdbx_dist_value / _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_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
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.6Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEASE INHIBITOR SGPI-1
B: CATIONIC TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3564
Polymers27,2572
Non-polymers992
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-18.1 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.910, 63.610, 43.870
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide PROTEASE INHIBITOR SGPI-1 / PROTEASE INHIBITOR SGPI-1 / SCHISTOCERCA GREGARIA TRYPSIN INHIBITOR / PROTEASE INHIBITOR SGPI-2 / ...PROTEASE INHIBITOR SGPI-1 / SCHISTOCERCA GREGARIA TRYPSIN INHIBITOR / PROTEASE INHIBITOR SGPI-2 / SCHISTOCERCA GREGARIA CHYMOTRYPSIN INHIBITOR / SGTI / SGCI


Mass: 3932.404 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-54 / Source method: obtained synthetically / Details: IN VITRO EVOLVED SEQUENCE WITH THE FOLLOWING / Source: (synth.) SCHISTOCERCA GREGARIA (desert locust) / References: UniProt: O46162
#2: Protein CATIONIC TRYPSIN / BETA-TRYPSIN / ALPHA-TRYPSIN CHAIN 1 / ALPHA-TRYPSIN CHAIN 2


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Cell: ACINAR CELLS / Organ: PANCREAS / Tissue: GLANDULAR / References: UniProt: P00760, trypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN VITRO EVOLVED SEQUENCE FOR CHAIN A.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.9 % / Description: NONE
Crystal growpH: 4.6
Details: EQUAL AMOUNT OF PROTEIN SOLUTION (9.1 MG/ML PROTEIN COMPLEX IN 0.5 MM MES PH 6.0 BUFFER) AND PRECIPITANT SOLUTION (30% PEG 4000, 0.3 M AMMONIUM ACETATE, 0.1 M NA-ACETATE PH 4.6) WERE MIXED ...Details: EQUAL AMOUNT OF PROTEIN SOLUTION (9.1 MG/ML PROTEIN COMPLEX IN 0.5 MM MES PH 6.0 BUFFER) AND PRECIPITANT SOLUTION (30% PEG 4000, 0.3 M AMMONIUM ACETATE, 0.1 M NA-ACETATE PH 4.6) WERE MIXED AND EQUILIBRATED AGAINST 0.5 ML PRECIPITANT SOLUTION.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 0.93→43.8 Å / Num. obs: 135272 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.9
Reflection shellResolution: 0.93→0.98 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 54

-
Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K1J

1k1j


Resolution: 0.93→10 Å / Num. parameters: 20959 / Num. restraintsaints: 25983 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: ASP-102, HIS-57, SER-195, ASP-194, GLY-193, SER-214 AND SCISSILE PEPTIDE BOND OF INHIBITOR
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.044. THE STRUCTURE WAS REFINED USING UNMERGED REFLECTIONS IN SHELX. THIS DATASET IS INCLUDED WITH THE MAIN STRUCTURE FACTOR FILE ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.044. THE STRUCTURE WAS REFINED USING UNMERGED REFLECTIONS IN SHELX. THIS DATASET IS INCLUDED WITH THE MAIN STRUCTURE FACTOR FILE R2XTTSF AS A SECOND DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1397 2035 1.6 %RANDOM
all0.1168 122128 --
obs--91 %-
Refine analyzeNum. disordered residues: 21 / Occupancy sum hydrogen: 1820.58 / Occupancy sum non hydrogen: 2225.9
Refinement stepCycle: LAST / Resolution: 0.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 5 350 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0346
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.121
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0.116

+
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