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- PDB-1y43: crystal structure of aspergilloglutamic peptidase from Aspergillu... -

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Basic information

Entry
Database: PDB / ID: 1y43
Titlecrystal structure of aspergilloglutamic peptidase from Aspergillus niger
Components
  • Aspergillopepsin II heavy chain
  • Aspergillopepsin II light chain
KeywordsHYDROLASE / aspergillopepsin II / proctase A / beta sandwich structure
Function / homology
Function and homology information


aspergillopepsin II / glutamic-type endopeptidase activity / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase G1 / Peptidase G1 / Peptidase G1 superfamily / Peptidase A4 family / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAspergillus niger var. macrosporus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.4 Å
AuthorsSasaki, H. / Nakagawa, A. / Iwata, S. / Muramatsu, T. / Suganuma, M. / Sawano, Y. / Kojima, M. / Kubota, K. / Takahashi, K.
CitationJournal: Proc.Jpn.Acad.,Ser.B / Year: 2004
Title: The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger
Authors: Sasaki, H. / Nakagawa, A. / Muramatsu, T. / Suganuma, M. / Sawano, Y. / Kojima, M. / Kubota, K. / Takahashi, K. / Tanokura, M.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspergillopepsin II light chain
B: Aspergillopepsin II heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7727
Polymers22,2912
Non-polymers4805
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-90 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.1, 70.7, 38.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Aspergillopepsin II light chain / / Acid protease A / Proctase A


Mass: 3919.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger var. macrosporus (mold) / Species: Aspergillus niger / Strain: Var. Macrosporus / References: UniProt: P24665, aspergillopepsin II
#2: Protein Aspergillopepsin II heavy chain / / Acid protease A / Proctase A


Mass: 18372.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger var. macrosporus (mold) / Species: Aspergillus niger / Strain: Var. Macrosporus / References: UniProt: P24665, aspergillopepsin II
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / 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: 1.64 Å3/Da / Density % sol: 26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 2.1
Details: ammonium sulfate, dimethyl sulfoxide, glycine, pH 2.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 30, 1993
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 29424 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.44 Å / % possible all: 82.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MLPHAREphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.4→10 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 2946 RANDOM
Rwork0.197 --
obs0.197 29266 -
all-29266 -
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 25 128 1661
LS refinement shellResolution: 1.4→1.46 Å
RfactorNum. reflection
Rfree0.2544 281
Rwork0.2558 -
obs-2802

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