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- PDB-1onx: Crystal structure of isoaspartyl dipeptidase from escherichia col... -

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Basic information

Entry
Database: PDB / ID: 1onx
TitleCrystal structure of isoaspartyl dipeptidase from escherichia coli complexed with aspartate
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / amidohydrolase / metalloprotease
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / 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 ...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
ASPARTIC ACID / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)82,8638
Polymers82,3362
Non-polymers5286
Water4,630257
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)331,45332
Polymers329,3428
Non-polymers2,11124
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 area29950 Å2
ΔGint-152 kcal/mol
Surface area95180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.100, 119.100, 138.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological unit is an octamer. It is generated by expanding the crystallographic independent unit around the crystallographic 4-fold axis using the following three transformations: (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 1.000 0.000 0.000 ROTATION MATRIX -1.000 0.000 0.000 0.000 -1.000 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

#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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.89 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG8000, 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: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 20, 2003 / Details: supper "long" mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 55201 / Num. obs: 55201 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.082 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 5640 / Rsym value: 0.263 / % possible all: 75.4
Reflection
*PLUS
Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 75.4 % / Num. unique obs: 5640 / Rmerge(I) obs: 0.263

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Processing

Software
NameVersionClassification
FRAMBOdata collection
XDSdata reduction
AMoREphasing
TNT5Erefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ONW

1onw


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5583 -random
Rwork0.177 ---
all0.182 55201 --
obs0.182 55201 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5766 0 22 257 6045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.3
Software
*PLUS
Name: 'TNT V.' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Num. reflection obs: 49618 / 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_deg17.1
X-RAY DIFFRACTIONt_planar_d0.008
X-RAY DIFFRACTIONt_plane_restr0.012

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