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- PDB-7f5q: The crystal structure of VyPAL2 peptide asparaginyl ligase in its... -

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Basic information

Entry
Database: PDB / ID: 7f5q
TitleThe crystal structure of VyPAL2 peptide asparaginyl ligase in its active enzyme form
ComponentsPeptide Asparaginyl Ligases
KeywordsPLANT PROTEIN / AEP / Legumain / VyPAL2
Function / homology
Function and homology information


vacuolar protein processing / vacuole / 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
Similarity search - Domain/homology
Peptide Asparaginyl Ligases
Similarity search - Component
Biological speciesViola philippica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHu, S. / Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2016-T3-1-003 Singapore
CitationJournal: Plant Cell / Year: 2022
Title: Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase.
Authors: Hu, S. / El Sahili, A. / Kishore, S. / Wong, Y.H. / Hemu, X. / Goh, B.C. / Zhipei, S. / Wang, Z. / Tam, J.P. / Liu, C.F. / Lescar, J.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: 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
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _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 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2May 1, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide Asparaginyl Ligases
B: Peptide Asparaginyl Ligases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,96115
Polymers62,2662
Non-polymers2,69613
Water6,539363
1
A: Peptide Asparaginyl Ligases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2866
Polymers31,1331
Non-polymers1,1535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint12 kcal/mol
Surface area12030 Å2
MethodPISA
2
B: Peptide Asparaginyl Ligases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6759
Polymers31,1331
Non-polymers1,5428
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint14 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.570, 63.880, 151.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 51 - 329 / Label seq-ID: 2 - 279

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptide Asparaginyl Ligases


Mass: 31132.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: D171 (forming SNN), residue 172 is HD0 (HIS + SNN) / Source: (gene. exp.) Viola philippica (plant) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A509GV09

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 370 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.3→48.88 Å / Num. obs: 28255 / % possible obs: 99.96 % / Redundancy: 10.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.419 / Net I/σ(I): 7.51
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2779 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IDV

6idv


Resolution: 2.3→48.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.862 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.331 / ESU R Free: 0.215 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2174 1351 5 %
Rwork0.1748 26904 -
all0.176 --
obs-28250 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.446 Å20 Å20 Å2
2--1.373 Å20 Å2
3---0.073 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4327 0 192 363 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124639
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.696293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37324.408211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87815696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7581510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023520
X-RAY DIFFRACTIONr_nbd_refined0.2080.22066
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.24
X-RAY DIFFRACTIONr_mcbond_it1.7942.5522230
X-RAY DIFFRACTIONr_mcangle_it2.8513.8182781
X-RAY DIFFRACTIONr_scbond_it3.1832409
X-RAY DIFFRACTIONr_scangle_it4.9244.3653512
X-RAY DIFFRACTIONr_lrange_it6.57935.9756929
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.059221
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.073030.0501
12BX-RAY DIFFRACTIONLocal ncs0.073030.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.266840.2531984X-RAY DIFFRACTION99.9517
2.36-2.4240.269740.2621919X-RAY DIFFRACTION100
2.424-2.4940.273980.261839X-RAY DIFFRACTION100
2.494-2.5710.268920.2331816X-RAY DIFFRACTION100
2.571-2.6550.263730.2141770X-RAY DIFFRACTION100
2.655-2.7480.2651140.2011650X-RAY DIFFRACTION100
2.748-2.8520.243810.1991633X-RAY DIFFRACTION100
2.852-2.9680.223780.1781583X-RAY DIFFRACTION99.9398
2.968-3.10.227870.1611529X-RAY DIFFRACTION100
3.1-3.2510.184650.161439X-RAY DIFFRACTION100
3.251-3.4270.214820.151369X-RAY DIFFRACTION100
3.427-3.6340.204650.1511317X-RAY DIFFRACTION100
3.634-3.8840.183570.1351258X-RAY DIFFRACTION100
3.884-4.1950.166560.1281166X-RAY DIFFRACTION100
4.195-4.5940.157530.1211089X-RAY DIFFRACTION100
4.594-5.1340.18540.134957X-RAY DIFFRACTION100
5.134-5.9230.236530.166867X-RAY DIFFRACTION100
5.923-7.2430.231240.177766X-RAY DIFFRACTION100
7.243-10.1970.229440.158588X-RAY DIFFRACTION100
10.197-48.880.177180.263365X-RAY DIFFRACTION99.2228

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