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- PDB-6dhi: Butelase 1: Auto-Catalytic Cleavage as an Evolutionary Constraint... -

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Basic information

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


legumain / vacuolar protein processing / vacuole / ligase activity / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / 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
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein
Asparaginyl 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


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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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)

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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

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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 %

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