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- PDB-1pok: Crystal structure of Isoaspartyl Dipeptidase -

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Basic information

Entry
Database: PDB / ID: 1pok
TitleCrystal 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 / cytosol / cytoplasm
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 ...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
ASPARAGINE / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,05410
Polymers82,3362
Non-polymers7188
Water1,60389
1
B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5275
Polymers41,1681
Non-polymers3594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5275
Polymers41,1681
Non-polymers3594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,21440
Polymers329,3428
Non-polymers2,87232
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
crystal symmetry operation5_646-x+3/2,y-1/2,-z+11
crystal symmetry operation6_566x+1/2,-y+3/2,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_766-y+2,-x+1,-z+11
Buried area32350 Å2
ΔGint-853 kcal/mol
Surface area88490 Å2
MethodPISA
4
A: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,05410
Polymers82,3362
Non-polymers7188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2990 Å2
ΔGint-187 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.475, 117.475, 137.955
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 %

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Data collection

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: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.209
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 32 89 5655

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