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

ID or keywords:

Entry

Database: PDB / ID: 8dqn

Title

Crystal structure of isoaspartyl dipeptidase from Leucothrix mucor DSM2157

Components

Isoaspartyl dipeptidase

Keywords

HYDROLASE / IadA

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Leucothrix mucor DSM 2157 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sharon, I. / Schmeing, T.M.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	Jul 19, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqn ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqn	HTTPS FTP

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Related structure data

Related structure data	8dqmC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

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

338 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	A	A	2 - 388	2 - 388
2	1	GLU	GLU	B	B	2 - 388	2 - 388
1	2	GLU	GLU	A	A	2 - 388	2 - 388
2	2	GLU	GLU	C	C	2 - 388	2 - 388
1	3	GLU	GLU	A	A	2 - 388	2 - 388
2	3	GLU	GLU	D	D	2 - 388	2 - 388
1	4	GLU	GLU	A	A	2 - 388	2 - 388
2	4	GLU	GLU	E	E	2 - 388	2 - 388
1	5	PHE	PHE	A	A	2 - 387	2 - 387
2	5	PHE	PHE	F	F	2 - 387	2 - 387
1	6	GLU	GLU	A	A	2 - 388	2 - 388
2	6	GLU	GLU	G	G	2 - 388	2 - 388
1	7	GLU	GLU	A	A	2 - 388	2 - 388
2	7	GLU	GLU	H	H	2 - 388	2 - 388
1	8	GLU	GLU	B	B	2 - 388	2 - 388
2	8	GLU	GLU	C	C	2 - 388	2 - 388
1	9	GLU	GLU	B	B	2 - 388	2 - 388
2	9	GLU	GLU	D	D	2 - 388	2 - 388
1	10	PHE	PHE	B	B	2 - 387	2 - 387
2	10	PHE	PHE	E	E	2 - 387	2 - 387
1	11	GLU	GLU	B	B	2 - 388	2 - 388
2	11	GLU	GLU	F	F	2 - 388	2 - 388
1	12	GLU	GLU	B	B	2 - 388	2 - 388
2	12	GLU	GLU	G	G	2 - 388	2 - 388
1	13	GLU	GLU	B	B	2 - 388	2 - 388
2	13	GLU	GLU	H	H	2 - 388	2 - 388
1	14	GLU	GLU	C	C	2 - 388	2 - 388
2	14	GLU	GLU	D	D	2 - 388	2 - 388
1	15	GLU	GLU	C	C	2 - 389	2 - 389
2	15	GLU	GLU	E	E	2 - 389	2 - 389
1	16	GLU	GLU	C	C	2 - 389	2 - 389
2	16	GLU	GLU	F	F	2 - 389	2 - 389
1	17	GLU	GLU	C	C	2 - 388	2 - 388
2	17	GLU	GLU	G	G	2 - 388	2 - 388
1	18	GLU	GLU	C	C	2 - 388	2 - 388
2	18	GLU	GLU	H	H	2 - 388	2 - 388
1	19	PHE	PHE	D	D	2 - 387	2 - 387
2	19	PHE	PHE	E	E	2 - 387	2 - 387
1	20	GLU	GLU	D	D	2 - 388	2 - 388
2	20	GLU	GLU	F	F	2 - 388	2 - 388
1	21	GLU	GLU	D	D	2 - 388	2 - 388
2	21	GLU	GLU	G	G	2 - 388	2 - 388
1	22	GLU	GLU	D	D	2 - 388	2 - 388
2	22	GLU	GLU	H	H	2 - 388	2 - 388
1	23	GLU	GLU	E	E	2 - 389	2 - 389
2	23	GLU	GLU	F	F	2 - 389	2 - 389
1	24	GLU	GLU	E	E	2 - 388	2 - 388
2	24	GLU	GLU	G	G	2 - 388	2 - 388
1	25	PHE	PHE	E	E	2 - 387	2 - 387
2	25	PHE	PHE	H	H	2 - 387	2 - 387
1	26	GLU	GLU	F	F	2 - 388	2 - 388
2	26	GLU	GLU	G	G	2 - 388	2 - 388
1	27	GLU	GLU	F	F	2 - 388	2 - 388
2	27	GLU	GLU	H	H	2 - 388	2 - 388
1	28	GLU	GLU	G	G	2 - 388	2 - 388
2	28	GLU	GLU	H	H	2 - 388	2 - 388

NCS ensembles :

#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 / Glycerol 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 / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3053 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.3 Å³/Da / Density % sol: 62.71 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.56 M NaH2PO4 and 1.04 M K2HPO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.8→118.34 Å / Num. obs: 386931 / % possible obs: 98.2 % / Redundancy: 13.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.1 / Net I/σ(I): 9.68
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 13.2 % / R_merge(I) obs: 0.868 / Mean I/σ(I) obs: 0.56 / Num. unique obs: 38129 / CC_1/2: 0.895 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→118.34 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18695	18699	4.8 %	RANDOM
R_work	0.16624	-	-	-
obs	0.16724	368266	98.16 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.635 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.45 Å²	0 Å²	-0 Å²
2-	-	-0.88 Å²	0 Å²
3-	-	-	0.43 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→118.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22786	0	104	3053	25943

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	23303
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	22379
X-RAY DIFFRACTION	r_angle_refined_deg	1.614	1.636	31663
X-RAY DIFFRACTION	r_angle_other_deg	1.411	1.574	51523
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.006	5	3040
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.638	22.19	1041
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.485	15	3774
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.745	15	136
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	3158
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	26308
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4924
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.571	2.864	12205
X-RAY DIFFRACTION	r_mcbond_other	2.571	2.864	12204
X-RAY DIFFRACTION	r_mcangle_it	3.742	4.277	15230
X-RAY DIFFRACTION	r_mcangle_other	3.742	4.278	15231
X-RAY DIFFRACTION	r_scbond_it	4.547	3.289	11098
X-RAY DIFFRACTION	r_scbond_other	4.511	3.277	11065
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.444	4.76	16386
X-RAY DIFFRACTION	r_long_range_B_refined	7.503	35.617	26441
X-RAY DIFFRACTION	r_long_range_B_other	7.243	34.498	25335
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11963	0.04
1	2	B	11963	0.04
2	1	A	12093	0.04
2	2	C	12093	0.04
3	1	A	12016	0.03
3	2	D	12016	0.03
4	1	A	12031	0.04
4	2	E	12031	0.04
5	1	A	11997	0.04
5	2	F	11997	0.04
6	1	A	11994	0.03
6	2	G	11994	0.03
7	1	A	11984	0.04
7	2	H	11984	0.04
8	1	B	11973	0.04
8	2	C	11973	0.04
9	1	B	11900	0.04
9	2	D	11900	0.04
10	1	B	11896	0.04
10	2	E	11896	0.04
11	1	B	11967	0.04
11	2	F	11967	0.04
12	1	B	11934	0.04
12	2	G	11934	0.04
13	1	B	11922	0.04
13	2	H	11922	0.04
14	1	C	11985	0.04
14	2	D	11985	0.04
15	1	C	12056	0.03
15	2	E	12056	0.03
16	1	C	12084	0.04
16	2	F	12084	0.04
17	1	C	11986	0.03
17	2	G	11986	0.03
18	1	C	11995	0.03
18	2	H	11995	0.03
19	1	D	11917	0.04
19	2	E	11917	0.04
20	1	D	11955	0.04
20	2	F	11955	0.04
21	1	D	11959	0.04
21	2	G	11959	0.04
22	1	D	11954	0.04
22	2	H	11954	0.04
23	1	E	12013	0.04
23	2	F	12013	0.04
24	1	E	11989	0.03
24	2	G	11989	0.03
25	1	E	11910	0.04
25	2	H	11910	0.04
26	1	F	11957	0.04
26	2	G	11957	0.04
27	1	F	11957	0.04
27	2	H	11957	0.04
28	1	G	11977	0.03
28	2	H	11977	0.03

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	1410	-
R_work	0.354	26767	-
obs	-	-	97.34 %

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