PDB-7ypp: Structural basis of a superoxide dismutase from a tardigrade, Ram...

ID or keywords:

Entry

Database: PDB / ID: 7ypp

Title

Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.

Components

Superoxide dismutase [Cu-Zn]

Keywords

OXIDOREDUCTASE / superoxide dismutase / SOD / CuZnSOD / Ramazzottius varieornatus / METAL BINDING PROTEIN

Function / homology

Function and homology information

superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / copper ion binding / protein homodimerization activity / zinc ion binding / identical protein binding
Similarity search - Function

Biological species

Ramazzottius varieornatus (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Sim, K.-S. / Fukuda, Y. / Inoue, T.

Funding support

Japan, 2items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.
Authors: Sim, K.S. / Inoue, T.

History

Deposition	Aug 4, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ypp.cif.gz	202.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7ypp.ent.gz	157.4 KB	Display	PDB format
PDBx/mmJSON format	7ypp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ypp_validation.pdf.gz	6.1 MB	Display	wwPDB validaton report
Full document	7ypp_full_validation.pdf.gz	6.1 MB	Display
Data in XML	7ypp_validation.xml.gz	39.1 KB	Display
Data in CIF	7ypp_validation.cif.gz	56 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypp ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypp	HTTPS FTP

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Related structure data

Related structure data	7yprC 1to4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#94 - Oct 2007 Superoxide Dismutase similarity (8)

Deposited unit

A: Superoxide dismutase [Cu-Zn]

C: Superoxide dismutase [Cu-Zn]

D: Superoxide dismutase [Cu-Zn]

E: Superoxide dismutase [Cu-Zn]

B: Superoxide dismutase [Cu-Zn]

F: Superoxide dismutase [Cu-Zn]

hetero molecules

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

1

A: Superoxide dismutase [Cu-Zn]

B: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author&software
40.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Superoxide dismutase [Cu-Zn]

D: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author&software
40.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Superoxide dismutase [Cu-Zn]

hetero molecules

F: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author&software
40.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.102, 68.049, 68.135
Angle α, β, γ (deg.)	94.895, 108.385, 114.400
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
2	1	1	VAL	VAL	VAL	VAL	C	B	30 - 194	30 - 194
3	2	2	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
4	2	2	VAL	VAL	VAL	VAL	D	C	30 - 194	30 - 194
5	3	3	LEU	LEU	TYR	TYR	A	A	33 - 193	33 - 193
6	3	3	LEU	LEU	TYR	TYR	E	D	33 - 193	33 - 193
7	4	4	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
8	4	4	VAL	VAL	VAL	VAL	B	E	30 - 194	30 - 194
9	5	5	PHE	PHE	TYR	TYR	A	A	34 - 193	34 - 193
10	5	5	PHE	PHE	TYR	TYR	F	F	34 - 193	34 - 193
11	6	6	VAL	VAL	VAL	VAL	C	B	30 - 194	30 - 194
12	6	6	VAL	VAL	VAL	VAL	D	C	30 - 194	30 - 194
13	7	7	LEU	LEU	VAL	VAL	C	B	33 - 194	33 - 194
14	7	7	LEU	LEU	VAL	VAL	E	D	33 - 194	33 - 194
15	8	8	VAL	VAL	VAL	VAL	C	B	30 - 194	30 - 194
16	8	8	VAL	VAL	VAL	VAL	B	E	30 - 194	30 - 194
17	9	9	PHE	PHE	TYR	TYR	C	B	34 - 193	34 - 193
18	9	9	PHE	PHE	TYR	TYR	F	F	34 - 193	34 - 193
19	10	10	LEU	LEU	TYR	TYR	D	C	33 - 193	33 - 193
20	10	10	LEU	LEU	TYR	TYR	E	D	33 - 193	33 - 193
21	11	11	VAL	VAL	VAL	VAL	D	C	30 - 194	30 - 194
22	11	11	VAL	VAL	VAL	VAL	B	E	30 - 194	30 - 194
23	12	12	PHE	PHE	TYR	TYR	D	C	34 - 193	34 - 193
24	12	12	PHE	PHE	TYR	TYR	F	F	34 - 193	34 - 193
25	13	13	LEU	LEU	TYR	TYR	E	D	33 - 193	33 - 193
26	13	13	LEU	LEU	TYR	TYR	B	E	33 - 193	33 - 193
27	14	14	PHE	PHE	VAL	VAL	E	D	34 - 194	34 - 194
28	14	14	PHE	PHE	VAL	VAL	F	F	34 - 194	34 - 194
29	15	15	PHE	PHE	TYR	TYR	B	E	34 - 193	34 - 193
30	15	15	PHE	PHE	TYR	TYR	F	F	34 - 193	34 - 193

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Superoxide dismutase [Cu-Zn] Mass: 20129.818 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ramazzottius varieornatus (invertebrata) Gene: RvY_13070-1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0A1D1VU85, superoxide dismutase
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 42.08 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 26% PEG 8000, 0.1 M MES pH 6.0, 0.2 M calcium acetate, TCEP addictive

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.28 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28 Å / Relative weight: 1
Reflection	Resolution: 2.2→45.37 Å / Num. obs: 48587 / % possible obs: 95.6 % / Redundancy: 3.6 % / B_iso Wilson estimate: 27.5 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.1 / R_rim(I) all: 0.142 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.677 / Num. unique obs: 13486 / CC_1/2: 0.596 / R_pim(I) all: 0.677 / R_rim(I) all: 0.957 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TO4

1to4

Resolution: 2.2→45.3 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.924 / Cross valid method: FREE R-VALUE / ESU R: 0.314 / ESU R Free: 0.216 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2343	2354	4.862 %
R_work	0.1981	46066	-
all	0.2	-	-
obs	-	48420	96.045 %

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: 33.538 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	-0.004 Å²	0.001 Å²
2-	-	-0.006 Å²	-0.004 Å²
3-	-	-	0.004 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→45.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7069	0	14	498	7581

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7268
X-RAY DIFFRACTION	r_angle_refined_deg	1.241	1.629	9888
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.577	5	975
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.91	22.027	301
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.429	15	1090
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.92	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	991
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5493
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	3201
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	4913
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	538
X-RAY DIFFRACTION	r_metal_ion_refined	0.066	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.299	0.2	113
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.203	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.502	3.217	3915
X-RAY DIFFRACTION	r_mcangle_it	3.749	4.813	4885
X-RAY DIFFRACTION	r_scbond_it	3.217	3.437	3353
X-RAY DIFFRACTION	r_scangle_it	4.499	5.035	5003
X-RAY DIFFRACTION	r_lrange_it	6.992	45.362	10735
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.102	0.05	4678
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.089	0.05	4886
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.093	0.05	4712
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.101	0.05	4762
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.078	0.05	4639
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.098	0.05	4720
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.105	0.05	4513
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.071	0.05	4789
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.102	0.05	4468
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.093	0.05	4666
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.093	0.05	4807
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.094	0.05	4557
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.101	0.05	4610
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.076	0.05	4680
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.099	0.05	4556

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10238	0.05009
1	2	C	X-RAY DIFFRACTION	Local ncs	0.10238	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08866	0.0501
2	4	D	X-RAY DIFFRACTION	Local ncs	0.08866	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09252	0.0501
3	6	E	X-RAY DIFFRACTION	Local ncs	0.09252	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.10147	0.05009
4	8	B	X-RAY DIFFRACTION	Local ncs	0.10147	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07758	0.0501
5	10	F	X-RAY DIFFRACTION	Local ncs	0.07758	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.0984	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.0984	0.0501
7	13	C	X-RAY DIFFRACTION	Local ncs	0.10484	0.05009
7	14	E	X-RAY DIFFRACTION	Local ncs	0.10484	0.05009
8	15	C	X-RAY DIFFRACTION	Local ncs	0.07094	0.05011
8	16	B	X-RAY DIFFRACTION	Local ncs	0.07094	0.05011
9	17	C	X-RAY DIFFRACTION	Local ncs	0.10203	0.05009
9	18	F	X-RAY DIFFRACTION	Local ncs	0.10203	0.05009
10	19	D	X-RAY DIFFRACTION	Local ncs	0.093	0.0501
10	20	E	X-RAY DIFFRACTION	Local ncs	0.093	0.0501
11	21	D	X-RAY DIFFRACTION	Local ncs	0.09322	0.0501
11	22	B	X-RAY DIFFRACTION	Local ncs	0.09322	0.0501
12	23	D	X-RAY DIFFRACTION	Local ncs	0.09372	0.0501
12	24	F	X-RAY DIFFRACTION	Local ncs	0.09372	0.0501
13	25	E	X-RAY DIFFRACTION	Local ncs	0.10082	0.0501
13	26	B	X-RAY DIFFRACTION	Local ncs	0.10082	0.0501
14	27	E	X-RAY DIFFRACTION	Local ncs	0.07571	0.0501
14	28	F	X-RAY DIFFRACTION	Local ncs	0.07571	0.0501
15	29	B	X-RAY DIFFRACTION	Local ncs	0.09946	0.0501
15	30	F	X-RAY DIFFRACTION	Local ncs	0.09946	0.0501

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 (%)
2.2-2.257	0.323	186	0.277	3268	X-RAY DIFFRACTION	93.7568
2.257-2.319	0.283	182	0.264	3194	X-RAY DIFFRACTION	93.6477
2.319-2.386	0.301	173	0.255	3163	X-RAY DIFFRACTION	93.2886
2.386-2.459	0.264	140	0.248	3095	X-RAY DIFFRACTION	95.0073
2.459-2.54	0.319	161	0.253	3055	X-RAY DIFFRACTION	95.8855
2.54-2.629	0.304	149	0.24	2979	X-RAY DIFFRACTION	96.5432
2.629-2.728	0.234	144	0.217	2841	X-RAY DIFFRACTION	96.4771
2.728-2.839	0.242	130	0.215	2749	X-RAY DIFFRACTION	96.7406
2.839-2.965	0.279	143	0.218	2626	X-RAY DIFFRACTION	96.5481
2.965-3.109	0.24	133	0.205	2500	X-RAY DIFFRACTION	96.5176
3.109-3.277	0.277	111	0.187	2409	X-RAY DIFFRACTION	96.404
3.277-3.475	0.202	116	0.186	2253	X-RAY DIFFRACTION	96.4969
3.475-3.714	0.186	114	0.174	2125	X-RAY DIFFRACTION	97.5599
3.714-4.011	0.2	109	0.172	2059	X-RAY DIFFRACTION	98.1884
4.011-4.392	0.191	84	0.154	1835	X-RAY DIFFRACTION	97.6094
4.392-4.907	0.208	89	0.145	1679	X-RAY DIFFRACTION	98.3315
4.907-5.661	0.215	72	0.173	1480	X-RAY DIFFRACTION	97.5487
5.661-6.919	0.16	50	0.195	1220	X-RAY DIFFRACTION	96.7988
6.919-9.725	0.231	43	0.187	990	X-RAY DIFFRACTION	98.0076
9.725-45.3	0.186	25	0.218	532	X-RAY DIFFRACTION	96.5338

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