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- PDB-8dqn: Crystal structure of isoaspartyl dipeptidase from Leucothrix muco... -

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Basic information

Entry
Database: PDB / ID: 8dqn
TitleCrystal structure of isoaspartyl dipeptidase from Leucothrix mucor DSM2157
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / IadA
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesLeucothrix mucor DSM 2157 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: Isoaspartyl dipeptidase
D: Isoaspartyl dipeptidase
E: Isoaspartyl dipeptidase
F: Isoaspartyl dipeptidase
G: Isoaspartyl dipeptidase
H: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,17340
Polymers335,6308
Non-polymers2,54332
Water55,0003053
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35840 Å2
ΔGint-880 kcal/mol
Surface area90050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.493, 163.691, 170.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA2 - 3882 - 388
21GLUGLUBB2 - 3882 - 388
12GLUGLUAA2 - 3882 - 388
22GLUGLUCC2 - 3882 - 388
13GLUGLUAA2 - 3882 - 388
23GLUGLUDD2 - 3882 - 388
14GLUGLUAA2 - 3882 - 388
24GLUGLUEE2 - 3882 - 388
15PHEPHEAA2 - 3872 - 387
25PHEPHEFF2 - 3872 - 387
16GLUGLUAA2 - 3882 - 388
26GLUGLUGG2 - 3882 - 388
17GLUGLUAA2 - 3882 - 388
27GLUGLUHH2 - 3882 - 388
18GLUGLUBB2 - 3882 - 388
28GLUGLUCC2 - 3882 - 388
19GLUGLUBB2 - 3882 - 388
29GLUGLUDD2 - 3882 - 388
110PHEPHEBB2 - 3872 - 387
210PHEPHEEE2 - 3872 - 387
111GLUGLUBB2 - 3882 - 388
211GLUGLUFF2 - 3882 - 388
112GLUGLUBB2 - 3882 - 388
212GLUGLUGG2 - 3882 - 388
113GLUGLUBB2 - 3882 - 388
213GLUGLUHH2 - 3882 - 388
114GLUGLUCC2 - 3882 - 388
214GLUGLUDD2 - 3882 - 388
115GLUGLUCC2 - 3892 - 389
215GLUGLUEE2 - 3892 - 389
116GLUGLUCC2 - 3892 - 389
216GLUGLUFF2 - 3892 - 389
117GLUGLUCC2 - 3882 - 388
217GLUGLUGG2 - 3882 - 388
118GLUGLUCC2 - 3882 - 388
218GLUGLUHH2 - 3882 - 388
119PHEPHEDD2 - 3872 - 387
219PHEPHEEE2 - 3872 - 387
120GLUGLUDD2 - 3882 - 388
220GLUGLUFF2 - 3882 - 388
121GLUGLUDD2 - 3882 - 388
221GLUGLUGG2 - 3882 - 388
122GLUGLUDD2 - 3882 - 388
222GLUGLUHH2 - 3882 - 388
123GLUGLUEE2 - 3892 - 389
223GLUGLUFF2 - 3892 - 389
124GLUGLUEE2 - 3882 - 388
224GLUGLUGG2 - 3882 - 388
125PHEPHEEE2 - 3872 - 387
225PHEPHEHH2 - 3872 - 387
126GLUGLUFF2 - 3882 - 388
226GLUGLUGG2 - 3882 - 388
127GLUGLUFF2 - 3882 - 388
227GLUGLUHH2 - 3882 - 388
128GLUGLUGG2 - 3882 - 388
228GLUGLUHH2 - 3882 - 388

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Isoaspartyl dipeptidase


Mass: 41953.773 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leucothrix mucor DSM 2157 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: beta-aspartyl-peptidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3053 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.56 M NaH2PO4 and 1.04 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→118.34 Å / Num. obs: 386931 / % possible obs: 98.2 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.68
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 38129 / CC1/2: 0.895 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→118.34 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.172 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18695 18699 4.8 %RANDOM
Rwork0.16624 ---
obs0.16724 368266 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.635 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0 Å2
2---0.88 Å20 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.8→118.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22786 0 104 3053 25943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01323303
X-RAY DIFFRACTIONr_bond_other_d0.0010.01522379
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.63631663
X-RAY DIFFRACTIONr_angle_other_deg1.4111.57451523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00653040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.63822.191041
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.485153774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.74515136
X-RAY DIFFRACTIONr_chiral_restr0.0730.23158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024924
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5712.86412205
X-RAY DIFFRACTIONr_mcbond_other2.5712.86412204
X-RAY DIFFRACTIONr_mcangle_it3.7424.27715230
X-RAY DIFFRACTIONr_mcangle_other3.7424.27815231
X-RAY DIFFRACTIONr_scbond_it4.5473.28911098
X-RAY DIFFRACTIONr_scbond_other4.5113.27711065
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4444.7616386
X-RAY DIFFRACTIONr_long_range_B_refined7.50335.61726441
X-RAY DIFFRACTIONr_long_range_B_other7.24334.49825335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119630.04
12B119630.04
21A120930.04
22C120930.04
31A120160.03
32D120160.03
41A120310.04
42E120310.04
51A119970.04
52F119970.04
61A119940.03
62G119940.03
71A119840.04
72H119840.04
81B119730.04
82C119730.04
91B119000.04
92D119000.04
101B118960.04
102E118960.04
111B119670.04
112F119670.04
121B119340.04
122G119340.04
131B119220.04
132H119220.04
141C119850.04
142D119850.04
151C120560.03
152E120560.03
161C120840.04
162F120840.04
171C119860.03
172G119860.03
181C119950.03
182H119950.03
191D119170.04
192E119170.04
201D119550.04
202F119550.04
211D119590.04
212G119590.04
221D119540.04
222H119540.04
231E120130.04
232F120130.04
241E119890.03
242G119890.03
251E119100.04
252H119100.04
261F119570.04
262G119570.04
271F119570.04
272H119570.04
281G119770.03
282H119770.03
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 1410 -
Rwork0.354 26767 -
obs--97.34 %

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