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- PDB-1fy2: Aspartyl Dipeptidase -

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Basic information

Entry
Database: PDB / ID: 1fy2
TitleAspartyl Dipeptidase
ComponentsASPARTYL DIPEPTIDASE
KeywordsHYDROLASE / serine protease / peptidase / catalytic triad / strand-helix motif
Function / homology
Function and homology information


dipeptidase E / dipeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase S51, dipeptidase E / Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsHakansson, K. / Wang, A.H.-J. / Miller, C.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.
Authors: Hakansson, K. / Wang, A.H. / Miller, C.G.
#1: Journal: J.Bacteriol. / Year: 2000
Title: Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase
Authors: Lassy, R.A. / Miller, C.G.
#2: Journal: J.Bacteriol. / Year: 1994
Title: Cloning and nucleotide sequence of the cyclic AMP receptor protein-regulated Salmonella typhimurium pepE gene and crystallization of its product, an alpha-aspartyl dipeptidase
Authors: Conlin, C.A. / Hakansson, K. / Liljas, A. / Miller, C.G.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTYL DIPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9062
Polymers24,7931
Non-polymers1121
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.986, 42.690, 62.496
Angle α, β, γ (deg.)90.00, 106.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1189-

HOH

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Components

#1: Protein ASPARTYL DIPEPTIDASE


Mass: 24793.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSE380 / Production host: Escherichia coli (E. coli)
References: UniProt: P36936, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 5mg/ml enzyme, 50mM Tris, 50mM cacodylate, 1mM CdSO4, 2-10% PEG 35000, equilibrated against a NaCl solution, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion / Details: Conlin, C.A., (1994) J.Bacteriol., 176, 166.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-12 mg/mlprotein1drop
250 mMCHES1drop
350 mMcacodylate-NaOH1drop
41 mM1dropCdSO4
52.5 %PEG350001drop
650 mMCHES1reservoir
70.25 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 68270 / % possible obs: 93.6 % / Redundancy: 2 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.274 / Num. unique all: 5515 / % possible all: 76.1
Reflection
*PLUS
Num. measured all: 137483
Reflection shell
*PLUS
% possible obs: 76.1 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.2→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS_TOPPAR:protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3488 -freerflag (CCP4)
Rwork0.218 ---
all-72970 --
obs-68259 93.5 %-
Refinement stepCycle: LAST / Resolution: 1.2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 1 192 1877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_torsion_deg24.9
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.218 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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