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- PDB-4nok: Crystal structure of proenzyme asparaginyl endopeptidase (AEP)/Le... -

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Basic information

Entry
Database: PDB / ID: 4nok
TitleCrystal structure of proenzyme asparaginyl endopeptidase (AEP)/Legumain at pH 7.5
ComponentsLegumain
KeywordsHYDROLASE / new fold / asparaginyl endopeptidase / substrate / extracellular
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / MHC class II antigen presentation / response to acidic pH / dendritic spine organization ...Trafficking and processing of endosomal TLR / negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / MHC class II antigen presentation / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular region
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold ...Topoisomerase I; Chain A, domain 4 - #130 / : / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Topoisomerase I; Chain A, domain 4 / Rossmann fold - #1460 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhao, L. / Hua, T. / Ru, H. / Ni, X. / Shaw, N. / Jiao, L. / Ding, W. / Qu, L. / Ouyang, S. / Liu, Z.J.
CitationJournal: Cell Res. / Year: 2014
Title: Structural analysis of asparaginyl endopeptidase reveals the activation mechanism and a reversible intermediate maturation stage.
Authors: Zhao, L. / Hua, T. / Crowley, C. / Ru, H. / Ni, X. / Shaw, N. / Jiao, L. / Ding, W. / Qu, L. / Hung, L.W. / Huang, W. / Liu, L. / Ye, K. / Ouyang, S. / Cheng, G. / Liu, Z.J.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legumain


Theoretical massNumber of molelcules
Total (without water)50,2671
Polymers50,2671
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.081, 168.908, 49.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

21A-573-

HOH

31A-604-

HOH

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Components

#1: Protein Legumain / Asparaginyl endopeptidase / Protease / cysteine 1


Mass: 50266.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgmn, Prsc1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89017, legumain
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M succinic acid, pH 7.0, and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 17063 / Num. obs: 17063 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.973 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 865 5.07 %RANDOM
Rwork0.2022 ---
all0.2519 17063 --
obs0.2047 17063 98.96 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.563 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.2236 Å2-0 Å2
3---0.0365 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 0 128 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033332
X-RAY DIFFRACTIONf_angle_d0.7764520
X-RAY DIFFRACTIONf_dihedral_angle_d14.7611220
X-RAY DIFFRACTIONf_chiral_restr0.053491
X-RAY DIFFRACTIONf_plane_restr0.003582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.65620.30621580.2312642X-RAY DIFFRACTION100
2.6562-2.86080.28411330.21552695X-RAY DIFFRACTION100
2.8608-3.14770.24821400.21662693X-RAY DIFFRACTION100
3.1477-3.60080.25141460.19932703X-RAY DIFFRACTION100
3.6008-4.5280.25291430.18132621X-RAY DIFFRACTION96
4.528-19.97380.21881450.20152844X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.967 Å / Origin y: 22.5902 Å / Origin z: 47.835 Å
111213212223313233
T0.0452 Å2-0.0099 Å2-0.0066 Å2-0.0445 Å2-0.0127 Å2--0.0484 Å2
L0.129 °2-0.0102 °20.1342 °2-0.4226 °20.1791 °2--0.4661 °2
S0.0217 Å °-0.0095 Å °0.0019 Å °-0.0229 Å °-0.0381 Å °0.0441 Å °0.0336 Å °-0.0462 Å °-0.1094 Å °
Refinement TLS groupSelection details: all

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