[English] 日本語
Yorodumi
- PDB-6dhi: Butelase 1: Auto-Catalytic Cleavage as an Evolutionary Constraint... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dhi
TitleButelase 1: Auto-Catalytic Cleavage as an Evolutionary Constraint for Macrocyclizing Endopeptidases
ComponentsAsparaginyl endopeptidaseAsparagine endopeptidase
KeywordsPLANT PROTEIN / Hydrolase / Asparaginyl endopeptidase
Function / homology
Function and homology information


legumain / ligase activity / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Asparaginyl endopeptidase
Similarity search - Component
Biological speciesClitoria ternatea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBond, C.S. / Haywood, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160100107 Australia
CitationJournal: Plant J. / Year: 2019
Title: The macrocyclizing protease butelase 1 remains autocatalytic and reveals the structural basis for ligase activity.
Authors: James, A.M. / Haywood, J. / Leroux, J. / Ignasiak, K. / Elliott, A.G. / Schmidberger, J.W. / Fisher, M.F. / Nonis, S.G. / Fenske, R. / Bond, C.S. / Mylne, J.S.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 26, 2019Group: 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Asparaginyl endopeptidase
B: Asparaginyl endopeptidase
C: Asparaginyl endopeptidase
D: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)210,8044
Polymers210,8044
Non-polymers00
Water46826
1
A: Asparaginyl endopeptidase
C: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)105,4022
Polymers105,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Asparaginyl endopeptidase
D: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)105,4022
Polymers105,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.360, 147.687, 183.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24B
15A
25C
16A
26D
17B
27C
18B
28D
19B
29C
110B
210D
111C
211D
112C
212D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHRAA44 - 16336 - 155
21GLYGLYTHRTHRBB44 - 16336 - 155
12THRTHRTYRTYRAA45 - 16237 - 154
22THRTHRTYRTYRCC45 - 16237 - 154
13GLYGLYTHRTHRAA44 - 16336 - 155
23GLYGLYTHRTHRDD44 - 16336 - 155
14HISHISSERSERAA165 - 481157 - 473
24HISHISSERSERBB165 - 481157 - 473
15HISHISSERSERAA165 - 481157 - 473
25HISHISSERSERCC165 - 481157 - 473
16HISHISSERSERAA165 - 481157 - 473
26HISHISSERSERDD165 - 481157 - 473
17THRTHRTYRTYRBB45 - 16237 - 154
27THRTHRTYRTYRCC45 - 16237 - 154
18GLYGLYTHRTHRBB44 - 16336 - 155
28GLYGLYTHRTHRDD44 - 16336 - 155
19HISHISSERSERBB165 - 481157 - 473
29HISHISSERSERCC165 - 481157 - 473
110HISHISSERSERBB165 - 481157 - 473
210HISHISSERSERDD165 - 481157 - 473
111THRTHRTYRTYRCC45 - 16237 - 154
211THRTHRTYRTYRDD45 - 16237 - 154
112HISHISSERSERCC165 - 481157 - 473
212HISHISSERSERDD165 - 481157 - 473

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.621768, -0.641548, -0.449245), (-0.476357, 0.76508, -0.433286), (0.621682, -0.055403, -0.781308)152.60205, 104.22303, 364.0433

-
Components

#1: Protein
Asparaginyl endopeptidase / Asparagine endopeptidase / Cte peptide ligase


Mass: 52701.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitoria ternatea (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060D9Z7, legumain
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 0.2 M sodium chloride, and 0.1 M HEPES (pH 7.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→49.42 Å / Num. obs: 36031 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.24 Å / Redundancy: 7 % / Rmerge(I) obs: 1.33 / Num. unique obs: 4339 / CC1/2: 0.64 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h0i

5h0i


Resolution: 3.1→49.42 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.821 / SU B: 33.123 / SU ML: 0.566 / Cross valid method: THROUGHOUT / ESU R Free: 0.606 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30899 1844 5.1 %RANDOM
Rwork0.274 ---
obs0.27577 34123 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.784 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--2.02 Å20 Å2
3----5.44 Å2
Refinement stepCycle: 1 / Resolution: 3.1→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13158 0 0 26 13184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913511
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212001
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.94118318
X-RAY DIFFRACTIONr_angle_other_deg1.026327971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88851665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09524.482627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.779152176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3181550
X-RAY DIFFRACTIONr_chiral_restr0.0670.21934
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115151
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022727
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 127 -
Rwork0.387 2446 -
obs--99.96 %

+
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