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- PDB-2aqv: Crystal Structure of E. coli Isoaspartyl Dipeptidase mutant Y137F -

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Basic information

Entry
Database: PDB / ID: 2aqv
TitleCrystal Structure of E. coli Isoaspartyl Dipeptidase mutant Y137F
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / metallo-protease / dipeptidase
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
Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsMarti-Arbona, R. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
CitationJournal: Bioorg.Chem. / Year: 2005
Title: Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase.
Authors: Marti-Arbona, R. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 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)82,5656
Polymers82,3042
Non-polymers2624
Water6,684371
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)330,26124
Polymers329,2148
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 area29910 Å2
ΔGint-801 kcal/mol
Surface area91460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.100, 119.100, 138.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Detailshomo-octomer. Biological assembly is generated by rotation chains A&B around the 4-fold axis located at 1/2,0/z (59.5, 0, 37.55)

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Components

#1: Protein Isoaspartyl dipeptidase


Mass: 41151.758 Da / Num. of mol.: 2 / Mutation: Y137F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iadA / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): JDG1000(DE3)
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.: 371 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG8000, homopipes, madnesium chloride, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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: Sep 6, 2003 / Details: supper 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: 1.95→30 Å / Num. all: 71537 / Num. obs: 71537 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.065 / Net I/σ(I): 11.6
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7448 / Rsym value: 0.264 / % possible all: 81.8

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Processing

Software
NameVersionClassificationNB
TNTrefinement
PDB_EXTRACT1.7data extraction
FRAMBOdata collection
XDSdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1onw

1onw


Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 7119 -random
Rwork0.183 ---
all0.185 71537 --
obs0.185 71537 97.9 %-
Displacement parametersBiso mean: 28.224 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 4 371 5913

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