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- PDB-5zbi: Crystal structure of asparaginyl endopeptidases from Viola Canadensis -

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Basic information

Entry
Database: PDB / ID: 5zbi
TitleCrystal structure of asparaginyl endopeptidases from Viola Canadensis
ComponentsPeptide asparaginyl ligase
KeywordsPLANT PROTEIN / peptide ligase
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity
Similarity search - Function
Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide asparaginyl ligase
Similarity search - Component
Biological speciesViola canadensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWong, Y.H. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)MOE2016-T3-1-003 Singapore
CitationJournal: To Be Published
Title: Crystal structure of Peptide asparaginyl ligase from Viola canadensis
Authors: Wong, Y.H. / Lescar, J.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide asparaginyl ligase
B: Peptide asparaginyl ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0893
Polymers119,0662
Non-polymers231
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-9 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.470, 62.080, 82.910
Angle α, β, γ (deg.)90.00, 106.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptide asparaginyl ligase


Mass: 59532.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Viola canadensis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E113*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.55 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium Sulfate, Bis-Tris pH 5.5, PEG 3350.

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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 210r / Detector: CCD / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→88.3 Å / Num. obs: 53019 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 31.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.055 / Net I/σ(I): 12
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 30795 / CC1/2: 0.719 / Rpim(I) all: 0.372 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H0I

5h0i


Resolution: 2.09→44.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2661 5.01 %RANDOM
Rwork0.189 ---
obs0.191 53019 99.4 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.2224 Å20 Å21.2576 Å2
2---8.5283 Å20 Å2
3---7.3059 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.09→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6557 0 1 498 7056
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016721HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.059114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2281SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes972HARMONIC5
X-RAY DIFFRACTIONt_it6721HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion18.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion853SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8662SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2513 184 5.06 %
Rwork0.2136 3451 -
all0.2156 3635 -
obs--92.09 %

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