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- PDB-5h0i: Structure of OaAEP1 asparaginyl peptide ligase in its proenzyme form -

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Basic information

Entry
Database: PDB / ID: 5h0i
TitleStructure of OaAEP1 asparaginyl peptide ligase in its proenzyme form
ComponentsAsparaginyl endopeptidase
KeywordsHYDROLASE
Function / homology
Function and homology information


legumain / 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 / Rossmann fold - #1460 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Asparaginyl endopeptidase
Similarity search - Component
Biological speciesOldenlandia affinis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsYang, R. / Wong, Y.H. / Lescar, J. / Wu, B.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Nanyang Technological UniversityNAP SUG Singapore
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Engineering a Catalytically Efficient Recombinant Protein Ligase
Authors: Yang, R. / Wong, Y.H. / Nguyen, G.K.T. / Tam, J.P. / Lescar, J. / Wu, B.
History
DepositionOct 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Nov 23, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asparaginyl endopeptidase
B: Asparaginyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)98,7882
Polymers98,7882
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint0 kcal/mol
Surface area31140 Å2
Unit cell
Length a, b, c (Å)145.730, 70.210, 118.280
Angle α, β, γ (deg.)90.00, 117.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Asparaginyl endopeptidase


Mass: 49393.871 Da / Num. of mol.: 2 / Fragment: UNP residues 24-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oldenlandia affinis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N9JZ32, legumain
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 200mM NH4NO3, pH ~ 4.5, 13-15%(w/v) PEG 3,350 with 10%(v/v) glycerol or ethylene glycol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→71.72 Å / Num. obs: 34420 / % possible obs: 99.7 % / Redundancy: 3 % / Biso Wilson estimate: 63.02 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOK

4nok


Resolution: 2.56→71.72 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.419 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.249
RfactorNum. reflection% reflectionSelection details
Rfree0.224 530 1.54 %RANDOM
Rwork0.186 ---
obs0.187 34408 99.6 %-
Displacement parametersBiso mean: 68.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.0652 Å20 Å2-1.0402 Å2
2--11.9628 Å20 Å2
3----7.8976 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.56→71.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 0 305 6507
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016355HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198624HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2139SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes930HARMONIC5
X-RAY DIFFRACTIONt_it6355HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion20.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion810SEMIHARMONIC5
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_contact7578SEMIHARMONIC4
LS refinement shellResolution: 2.56→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.215 -1.54 %
Rwork0.211 2934 -
all0.211 2980 -
obs--99.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8177-0.71490.24582.9105-0.37510.7992-0.14870.0151-0.28610.34680.1524-0.2406-0.02050.1543-0.0037-0.09690.0546-0.0517-0.23830.0131-0.076312.7605-19.244627.604
22.4529-0.3952-0.3721.90890.08620.7730.04870.21080.3655-0.07630.07960.1136-0.1757-0.1527-0.1282-0.06550.05040.0278-0.19020.0645-0.0593-15.105213.636526.19
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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