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- PDB-1onw: Crystal structure of Isoaspartyl Dipeptidase from E. coli -

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Basic information

Entry
Database: PDB / ID: 1onw
TitleCrystal structure of Isoaspartyl Dipeptidase from E. coli
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / amidohydrolase / metalloprotease
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 / MIR / Resolution: 1.65 Å
AuthorsThoden, J.B. / Marti-Arbona, R. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2003
Title: High Resolution X-ray Structure of Isoaspartyl Dipeptidase from Escherichia coli
Authors: Thoden, J.B. / Marti-Arbona, R. / Raushel, F.M. / Holden, H.M.
History
DepositionMar 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

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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)82,93714
Polymers82,3362
Non-polymers60112
Water13,511750
1
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)331,74856
Polymers329,3428
Non-polymers2,40648
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area36190 Å2
ΔGint-908 kcal/mol
Surface area89350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.700, 116.700, 138.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-804-

MG

21A-1022-

HOH

31B-978-

HOH

41B-991-

HOH

51B-1191-

HOH

DetailsThe biological assembly is an octomer. It is generated by expanding the crystallographically independent unit around the 4-fold crystallographic axis. The three rotational & translational matrices used to generate the octamer are as follows: (I) TRANSLATION VECTOR IN fractions of cell edge 0.500 0.500 0.000 ROTATION MATRIX 0.000 -1.000 0.000 1.000 0.000 0.000 0.000 0.000 1.000 (II) TRANSLATION VECTOR IN fractions of cell edge 0.000 1.000 0.000 ROTATION MATRIX -1.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 1.000 TRANSLATION VECTOR IN fractions of cell edge -0.500 0.500 0.000 ROTATION MATRIX 0.000 1.000 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 (III)TRANSLATION VECTOR IN fractions of cell edge -0.500 0.500 0.000 ROTATION MATRIX 0.000 1.000 0.000 -1.000 0.000 0.000 0.000 0.000 1.000

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isoaspartyl dipeptidase


Mass: 41167.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: IADA OR B4328 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star
References: UniProt: P39377, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases

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Non-polymers , 6 types, 762 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.63 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG-8000, homopipes, magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 %PEG80001reservoir
2100 mMhomopipes1reservoirpH5.0
350-100 mM1reservoirMgCl2
411.0 mg/mlprotein1drop
550 mMTris1droppH8.1

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 12, 2003 / Details: goebel mirrors
RadiationMonochromator: goebel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 112776 / Num. obs: 112776 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rsym value: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 1.65→1.73 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 12288 / Rsym value: 0.347 / % possible all: 81.8
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 81.8 % / Num. unique obs: 12288 / Rmerge(I) obs: 0.347

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Processing

Software
NameVersionClassification
FRAMBOdata collection
SAINTdata reduction
SOLVEphasing
TNT5Erefinement
SAINTdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 11330 -random
Rwork0.178 ---
all0.182 112776 --
obs0.182 112776 98.2 %-
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 21 750 6349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.45
Refinement
*PLUS
Num. reflection obs: 101398 / Rfactor all: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.5
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.015

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