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- PDB-1ybq: Crystal structure of Escherichia coli isoaspartyl dipeptidase mut... -

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Basic information

Entry
Database: PDB / ID: 1ybq
TitleCrystal structure of Escherichia coli isoaspartyl dipeptidase mutant D285N complexed with beta-aspartylhistidine
Components(Isoaspartyl dipeptidase) x 2
KeywordsHYDROLASE / 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
L-BETA-ASPARTYLHISTIDINE / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMarti-Arbona, R. / Fresquet, V. / Thoden, J.B. / Davis, M.L. / Holden, H.M. / Raushel, F.M.
CitationJournal: Biochemistry / Year: 2005
Title: Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
Authors: Marti-Arbona, R. / Fresquet, V. / Thoden, J.B. / Davis, M.L. / Holden, H.M. / Raushel, F.M.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 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
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_conn_type / 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_conn_type.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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,0938
Polymers82,2912
Non-polymers8026
Water4,342241
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)332,37132
Polymers329,1628
Non-polymers3,20824
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 area36630 Å2
ΔGint-790 kcal/mol
Surface area92740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.300, 119.300, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is an octomer. It is generated by rotation of chains A and B around the crystallographic 4-fold axis located at 1/2, 0, 37.267

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Components

#1: Protein Isoaspartyl dipeptidase


Mass: 41123.773 Da / Num. of mol.: 1 / Mutation: D285N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iadA / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR
References: UniProt: P39377, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Isoaspartyl dipeptidase


Mass: 41166.773 Da / Num. of mol.: 1 / Mutation: D285N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iadA / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR
References: UniProt: P39377, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BDH / L-BETA-ASPARTYLHISTIDINE


Mass: 270.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.88 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG8000, homopipes, magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Apr 16, 2004 / 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→30 Å / Num. all: 61655 / Num. obs: 61655 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.054 / Net I/σ(I): 11
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6311 / Rsym value: 0.202 / % possible all: 75.6

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Processing

Software
NameClassification
FRAMBOdata collection
XDSdata reduction
TNTrefinement
XDSdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB 1ONW

1onw


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 6043 random
Rwork0.181 --
all0.185 61655 -
obs0.185 61655 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 42 241 6046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.3

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