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- PDB-8dqm: Crystal structure of isoaspartyl aminopeptidase from Roseivivax h... -

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Basic information

Entry
Database: PDB / ID: 8dqm
TitleCrystal structure of isoaspartyl aminopeptidase from Roseivivax halodurans DSM 15395
Components(Isoaspartyl aminopeptidase) x 2
KeywordsHYDROLASE / IaaA
Function / homologyPeptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Asparaginase
Function and homology information
Biological speciesRoseivivax halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSharon, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2023
Title: Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation.
Authors: Sharon, I. / Schmeing, T.M.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoaspartyl aminopeptidase
B: Isoaspartyl aminopeptidase
C: Isoaspartyl aminopeptidase
D: Isoaspartyl aminopeptidase
E: Isoaspartyl aminopeptidase
F: Isoaspartyl aminopeptidase
G: Isoaspartyl aminopeptidase
H: Isoaspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,82312
Polymers131,7318
Non-polymers924
Water2,666148
1
A: Isoaspartyl aminopeptidase
B: Isoaspartyl aminopeptidase
C: Isoaspartyl aminopeptidase
D: Isoaspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9116
Polymers65,8654
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-82 kcal/mol
Surface area20230 Å2
MethodPISA
2
E: Isoaspartyl aminopeptidase
F: Isoaspartyl aminopeptidase
G: Isoaspartyl aminopeptidase
H: Isoaspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9116
Polymers65,8654
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-82 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.222, 154.593, 197.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Isoaspartyl aminopeptidase / Asparaginase


Mass: 18660.852 Da / Num. of mol.: 4 / Fragment: N-terminal residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseivivax halodurans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X7EBZ8
#2: Protein
Isoaspartyl aminopeptidase / Asparaginase


Mass: 14271.830 Da / Num. of mol.: 4 / Fragment: C-terminal residues 178-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseivivax halodurans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X7EBZ8
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.91 Å3/Da / Density % sol: 68.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane pH 8.5, 0.2 M disodium malonate and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.522 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.522 Å / Relative weight: 1
ReflectionResolution: 2.6→98.96 Å / Num. obs: 59664 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.76
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 5893 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 2.7→98.96 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 2636 4.94 %Random selection
Rwork0.2432 ---
obs0.2445 53362 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→98.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8510 0 4 148 8662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138612
X-RAY DIFFRACTIONf_angle_d1.79711614
X-RAY DIFFRACTIONf_dihedral_angle_d10.4313089
X-RAY DIFFRACTIONf_chiral_restr0.091296
X-RAY DIFFRACTIONf_plane_restr0.0061567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.34851310.3372606X-RAY DIFFRACTION100
2.75-2.80.30451480.31852628X-RAY DIFFRACTION100
2.8-2.860.39021560.31132604X-RAY DIFFRACTION100
2.86-2.920.30961250.29332670X-RAY DIFFRACTION100
2.92-2.990.33181330.2972617X-RAY DIFFRACTION100
2.99-3.060.28851250.27622633X-RAY DIFFRACTION100
3.06-3.150.30561330.27442681X-RAY DIFFRACTION100
3.15-3.240.25931170.25992640X-RAY DIFFRACTION100
3.24-3.340.31011430.25412641X-RAY DIFFRACTION100
3.34-3.460.27661390.24162674X-RAY DIFFRACTION100
3.46-3.60.22921380.22172631X-RAY DIFFRACTION100
3.6-3.770.26431300.2222657X-RAY DIFFRACTION100
3.77-3.960.23461450.21372676X-RAY DIFFRACTION100
3.96-4.210.23581580.2112639X-RAY DIFFRACTION100
4.21-4.540.22571540.19472669X-RAY DIFFRACTION100
4.54-4.990.23711130.20062706X-RAY DIFFRACTION100
5-5.720.25381470.23142732X-RAY DIFFRACTION100
5.72-7.20.261540.24832726X-RAY DIFFRACTION100
7.2-98.960.27271470.26412896X-RAY DIFFRACTION100

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