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- PDB-1po9: Crytsal structure of isoaspartyl dipeptidase -

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Basic information

Entry
Database: PDB / ID: 1po9
TitleCrytsal structure of isoaspartyl dipeptidase
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / beta-aspartyl-peptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isoaspartyl-dipeptidase / Peptidase M38, beta-aspartyl dipeptidase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Isoaspartyl-dipeptidase / Peptidase M38, beta-aspartyl dipeptidase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJozic, D. / Kaiser, J.T. / Huber, R. / Bode, W. / Maskos, K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases.
Authors: Jozic, D. / Kaiser, J.T. / Huber, R. / Bode, W. / Maskos, K.
History
DepositionJun 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5976
Polymers82,3362
Non-polymers2624
Water9,404522
1
A: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2993
Polymers41,1681
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2993
Polymers41,1681
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,38924
Polymers329,3428
Non-polymers1,04716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area30480 Å2
ΔGint-795 kcal/mol
Surface area87980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.644, 116.644, 137.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Isoaspartyl dipeptidase


Mass: 41167.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P39377, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.83 Å3/Da / Density % sol: 56.55 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.198
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 4 522 6026

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