PDB-7d66: Crystal structure of retroviral protease-like domain of Ddi1 from...

ID or keywords:

Entry

Database: PDB / ID: 7d66

Title

Crystal structure of retroviral protease-like domain of Ddi1 from Toxoplasma gondii

Components

Ubiquitin family protein

Keywords

HYDROLASE / Retroviral protease

Function / homology

Function and homology information

aspartic-type endopeptidase activity / mitochondrion
Similarity search - Function

Biological species

Toxoplasma gondii GT1 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.126 Å

Authors

Biswas, I.B. / Killivalavan, A.K. / Suguna, K.S.

Funding support

India, 1items

Citation

Journal: Curr Res Struct Biol / Year: 2022
Title: Structural and functional insights into the DNA damage-inducible protein 1 (Ddi1) from protozoa.
Authors: Asaithambi, K. / Biswas, I. / Suguna, K.

History

Deposition	Sep 29, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Dec 7, 2022	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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.name
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7d66.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7d66.ent.gz	859.1 KB	Display	PDB format
PDBx/mmJSON format	7d66.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/7d66 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d66	HTTPS FTP

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Related structure data

Related structure data	7efyC 2i1aS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3pic-d 6at1-d 4fyx-d 1rai-d 2qg9-d 2fzc-d 1rad-d 5at1-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #81 - Sep 2006 Elongation Factors similarity (1)

Deposited unit

B: Ubiquitin family protein

A: Ubiquitin family protein

D: Ubiquitin family protein

C: Ubiquitin family protein

F: Ubiquitin family protein

E: Ubiquitin family protein

H: Ubiquitin family protein

G: Ubiquitin family protein

J: Ubiquitin family protein

I: Ubiquitin family protein

L: Ubiquitin family protein

K: Ubiquitin family protein

hetero molecules

175 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Ubiquitin family protein

A: Ubiquitin family protein

D: Ubiquitin family protein

C: Ubiquitin family protein

F: Ubiquitin family protein

E: Ubiquitin family protein

hetero molecules

defined by author
Evidence: gel filtration
87.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Ubiquitin family protein

G: Ubiquitin family protein

J: Ubiquitin family protein

I: Ubiquitin family protein

L: Ubiquitin family protein

K: Ubiquitin family protein

hetero molecules

defined by author
87.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.601, 184.601, 184.338
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Ubiquitin family protein / retroviral protease-like domain of Ddi1 Mass: 14466.896 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii GT1 (eukaryote) / Strain: ATCC 50853 / GT1 / Gene: TGGT1_304680 / Production host: Escherichia coli (E. coli) / References: UniProt: S7W9N7
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 585 / 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: 4.68 Å³/Da / Density % sol: 73.74 %
Crystal grow	Temperature: 293 K / Method: microbatch / Details: 2 M ammonium citrate tribasic, 30 % 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.99 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.12→65.27 Å / Num. obs: 176969 / % possible obs: 100 % / Redundancy: 8.6 % / CC_1/2: 0.99 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.126→2.182 Å / Num. unique obs: 8844 / CC_1/2: 0.365

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2I1A

2i1a

Resolution: 2.126→65.266 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.932 / SU B: 8.396 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2475	8844	4.997 %
R_work	0.1922	168125	-
all	0.195	-	-
obs	-	176969	99.688 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.448 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.886 Å²	-0 Å²	-0 Å²
2-	-	-8.886 Å²	-0 Å²
3-	-	-	17.773 Å²

Refinement step

Cycle: LAST / Resolution: 2.126→65.266 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11178	0	96	585	11859

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	11420
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	11178
X-RAY DIFFRACTION	r_angle_refined_deg	1.833	1.635	15352
X-RAY DIFFRACTION	r_angle_other_deg	1.464	1.583	25636
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.418	5	1428
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.989	22.109	512
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.095	15	2028
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.911	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	1553
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	12615
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2566
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	2118
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.226	0.2	11668
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	5522
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	6551
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	380
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.126	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.652	0.2	114
X-RAY DIFFRACTION	r_nbd_other	0.535	0.2	310
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.606	0.2	18
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.444	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	5.856	3.328	5790
X-RAY DIFFRACTION	r_mcbond_other	5.85	3.327	5789
X-RAY DIFFRACTION	r_mcangle_it	6.752	4.992	7192
X-RAY DIFFRACTION	r_mcangle_other	6.752	4.992	7193
X-RAY DIFFRACTION	r_scbond_it	6.212	3.44	5630
X-RAY DIFFRACTION	r_scbond_other	6.211	3.44	5631
X-RAY DIFFRACTION	r_scangle_it	7.112	5.127	8160
X-RAY DIFFRACTION	r_scangle_other	7.112	5.127	8161
X-RAY DIFFRACTION	r_lrange_it	7.732	63.737	43972
X-RAY DIFFRACTION	r_lrange_other	7.732	63.737	43973
X-RAY DIFFRACTION	r_rigid_bond_restr	5.042	3	22596
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.14	0.05	3190
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.155	0.05	3112
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.149	0.05	3141
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.139	0.05	3170
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.136	0.05	2956
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.143	0.05	3156
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.149	0.05	3182
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.156	0.05	3151
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.144	0.05	3218
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.148	0.05	3267
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.145	0.05	3157
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.143	0.05	3158
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.157	0.05	3082
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.136	0.05	3201
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.134	0.05	2879
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.141	0.05	3204
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.135	0.05	3203
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.14	0.05	3156
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.13	0.05	3304
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.14	0.05	3266
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.149	0.05	3164
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.158	0.05	3033
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.141	0.05	3055
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.125	0.05	2846
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.148	0.05	3103
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.142	0.05	3132
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.164	0.05	3033
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.154	0.05	3187
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.155	0.05	3175
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.154	0.05	3109
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.153	0.05	3063
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.144	0.05	2830
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.149	0.05	3038
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.151	0.05	3063
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.166	0.05	3001
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.154	0.05	3133
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.16	0.05	3122
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.158	0.05	3084
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.131	0.05	2867
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.144	0.05	3202
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.14	0.05	3112
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.155	0.05	3069
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.133	0.05	3141
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.147	0.05	3195
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.153	0.05	3084
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.145	0.05	2886
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.146	0.05	2928
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.158	0.05	2874
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.14	0.05	2836
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.142	0.05	2891
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.147	0.05	2897
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.145	0.05	3130
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.154	0.05	3061
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.145	0.05	3176
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.128	0.05	3249
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.145	0.05	3109
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.154	0.05	3132
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.138	0.05	3233
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.151	0.05	3197
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.149	0.05	3099
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.157	0.05	3136
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.157	0.05	3154
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.159	0.05	3083
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.137	0.05	3273
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.14	0.05	3177
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.153	0.05	3183

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.126-2.182	0.224	591	0.15	11830	X-RAY DIFFRACTION	95.8041
2.13-2.18	0.21	92	0.206	2155	X-RAY DIFFRACTION	99.6011
2.182-2.241	0.244	600	0.155	12078	X-RAY DIFFRACTION	100
2.241-2.306	0.244	706	0.166	11649	X-RAY DIFFRACTION	100
2.306-2.377	0.283	574	0.189	11363	X-RAY DIFFRACTION	100
2.377-2.455	0.28	488	0.187	11146	X-RAY DIFFRACTION	100
2.455-2.541	0.299	566	0.221	10643	X-RAY DIFFRACTION	100
2.541-2.637	0.301	646	0.2	10256	X-RAY DIFFRACTION	100
2.637-2.745	0.289	555	0.202	9893	X-RAY DIFFRACTION	100
2.745-2.867	0.292	530	0.211	9529	X-RAY DIFFRACTION	100
2.867-3.007	0.282	424	0.207	9190	X-RAY DIFFRACTION	100
3.007-3.169	0.269	448	0.207	8715	X-RAY DIFFRACTION	100
3.169-3.362	0.225	401	0.194	8279	X-RAY DIFFRACTION	100
3.362-3.593	0.242	423	0.193	7750	X-RAY DIFFRACTION	100
3.593-3.881	0.228	368	0.191	7255	X-RAY DIFFRACTION	100
3.881-4.251	0.226	375	0.184	6690	X-RAY DIFFRACTION	100
4.251-4.752	0.211	395	0.151	6028	X-RAY DIFFRACTION	100
4.752-5.486	0.204	283	0.178	5378	X-RAY DIFFRACTION	100
5.486-6.716	0.307	211	0.253	4652	X-RAY DIFFRACTION	99.9794
6.716-9.486	0.296	168	0.215	3646	X-RAY DIFFRACTION	100

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