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

ID or keywords:

Entry

Database: PDB / ID: 7ypr

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: 2.101 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	Dec 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ypr.cif.gz	209.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7ypr.ent.gz	166 KB	Display	PDB format
PDBx/mmJSON format	7ypr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7ypr_validation.pdf.gz	6.5 MB	Display	wwPDB validaton report
Full document	7ypr_full_validation.pdf.gz	6.5 MB	Display
Data in XML	7ypr_validation.xml.gz	40.5 KB	Display
Data in CIF	7ypr_validation.cif.gz	58 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypr ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypr	HTTPS FTP

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Related structure data

Related structure data	7yppC 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]

B: Superoxide dismutase [Cu-Zn]

C: Superoxide dismutase [Cu-Zn]

D: Superoxide dismutase [Cu-Zn]

E: 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]

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.825, 105.825, 76.956
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

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	ASN	ASN	TYR	TYR	A	A	31 - 193	31 - 193
2	1	1	ASN	ASN	TYR	TYR	B	B	31 - 193	31 - 193
3	2	2	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
4	2	2	VAL	VAL	VAL	VAL	C	C	30 - 194	30 - 194
5	3	3	ASN	ASN	TYR	TYR	A	A	31 - 193	31 - 193
6	3	3	ASN	ASN	TYR	TYR	D	D	31 - 193	31 - 193
7	4	4	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
8	4	4	VAL	VAL	VAL	VAL	E	E	30 - 194	30 - 194
9	5	5	VAL	VAL	VAL	VAL	A	A	30 - 194	30 - 194
10	5	5	VAL	VAL	VAL	VAL	F	F	30 - 194	30 - 194
11	6	6	ASN	ASN	TYR	TYR	B	B	31 - 193	31 - 193
12	6	6	ASN	ASN	TYR	TYR	C	C	31 - 193	31 - 193
13	7	7	ASN	ASN	VAL	VAL	B	B	31 - 194	31 - 194
14	7	7	ASN	ASN	VAL	VAL	D	D	31 - 194	31 - 194
15	8	8	ASN	ASN	TYR	TYR	B	B	31 - 193	31 - 193
16	8	8	ASN	ASN	TYR	TYR	E	E	31 - 193	31 - 193
17	9	9	ASN	ASN	TYR	TYR	B	B	31 - 193	31 - 193
18	9	9	ASN	ASN	TYR	TYR	F	F	31 - 193	31 - 193
19	10	10	ASN	ASN	TYR	TYR	C	C	31 - 193	31 - 193
20	10	10	ASN	ASN	TYR	TYR	D	D	31 - 193	31 - 193
21	11	11	VAL	VAL	VAL	VAL	C	C	30 - 194	30 - 194
22	11	11	VAL	VAL	VAL	VAL	E	E	30 - 194	30 - 194
23	12	12	VAL	VAL	VAL	VAL	C	C	30 - 194	30 - 194
24	12	12	VAL	VAL	VAL	VAL	F	F	30 - 194	30 - 194
25	13	13	ASN	ASN	TYR	TYR	D	D	31 - 193	31 - 193
26	13	13	ASN	ASN	TYR	TYR	E	E	31 - 193	31 - 193
27	14	14	ASN	ASN	TYR	TYR	D	D	31 - 193	31 - 193
28	14	14	ASN	ASN	TYR	TYR	F	F	31 - 193	31 - 193
29	15	15	VAL	VAL	VAL	VAL	E	E	30 - 194	30 - 194
30	15	15	VAL	VAL	VAL	VAL	F	F	30 - 194	30 - 194

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: 20168.834 Da / Num. of mol.: 6 / Mutation: V87H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ramazzottius varieornatus (invertebrata) Gene: RvY_13070-1, RvY_13070.1, RvY_13070 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0A1D1VU85, superoxide dismutase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.06 Å³/Da / Density % sol: 40.17 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG 6000, 0.1 M MES pH 6.5, 0.2 M Potassium chloride, and 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: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.1→45.89 Å / Num. obs: 56839 / % possible obs: 99.6 % / Redundancy: 4.6 % / B_iso Wilson estimate: 25.7 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / R_pim(I) all: 0.026 / R_rim(I) all: 0.057 / Net I/σ(I): 18.4
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.225 / Mean I/σ(I) obs: 7 / Num. unique obs: 4490 / CC_1/2: 0.954 / R_pim(I) all: 0.121 / R_rim(I) all: 0.256 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.101→45.866 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.234 / ESU R Free: 0.188 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2281	2800	5.002 %
R_work	0.1803	53183	-
all	0.183	-	-
obs	-	55983	99.653 %

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: 43.165 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.002 Å²	-0.001 Å²	-0 Å²
2-	-	-0.002 Å²	-0 Å²
3-	-	-	0.005 Å²

Refinement step

Cycle: LAST / Resolution: 2.101→45.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7210	0	13	427	7650

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	7641
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.626	10436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.48	5	1047
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.702	21.994	321
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.084	15	1153
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.867	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1043
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5893
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	3513
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	5151
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	469
X-RAY DIFFRACTION	r_metal_ion_refined	0.091	0.2	14
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.206	0.2	101
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.149	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	5.168	4.179	4119
X-RAY DIFFRACTION	r_mcangle_it	5.83	6.218	5186
X-RAY DIFFRACTION	r_scbond_it	6.173	4.444	3522
X-RAY DIFFRACTION	r_scangle_it	7.227	6.489	5249
X-RAY DIFFRACTION	r_lrange_it	7.775	58.464	11402
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.155	0.05	4778
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.141	0.05	4993
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.158	0.05	4757
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.175	0.05	4757
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.157	0.05	4885
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.142	0.05	4851
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.147	0.05	4983
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.153	0.05	4892
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.162	0.05	4711
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.148	0.05	4617
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.168	0.05	4619
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.15	0.05	4748
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.154	0.05	4834
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.163	0.05	4627
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.185	0.05	4634

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	0.15544	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.15544	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.14091	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.14091	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.1582	0.05007
3	6	D	X-RAY DIFFRACTION	Local ncs	0.1582	0.05007
4	7	A	X-RAY DIFFRACTION	Local ncs	0.17533	0.05007
4	8	E	X-RAY DIFFRACTION	Local ncs	0.17533	0.05007
5	9	A	X-RAY DIFFRACTION	Local ncs	0.15724	0.05007
5	10	F	X-RAY DIFFRACTION	Local ncs	0.15724	0.05007
6	11	B	X-RAY DIFFRACTION	Local ncs	0.14243	0.05008
6	12	C	X-RAY DIFFRACTION	Local ncs	0.14243	0.05008
7	13	B	X-RAY DIFFRACTION	Local ncs	0.14723	0.05008
7	14	D	X-RAY DIFFRACTION	Local ncs	0.14723	0.05008
8	15	B	X-RAY DIFFRACTION	Local ncs	0.15299	0.05007
8	16	E	X-RAY DIFFRACTION	Local ncs	0.15299	0.05007
9	17	B	X-RAY DIFFRACTION	Local ncs	0.16226	0.05007
9	18	F	X-RAY DIFFRACTION	Local ncs	0.16226	0.05007
10	19	C	X-RAY DIFFRACTION	Local ncs	0.14816	0.05007
10	20	D	X-RAY DIFFRACTION	Local ncs	0.14816	0.05007
11	21	C	X-RAY DIFFRACTION	Local ncs	0.16832	0.05006
11	22	E	X-RAY DIFFRACTION	Local ncs	0.16832	0.05006
12	23	C	X-RAY DIFFRACTION	Local ncs	0.15028	0.05007
12	24	F	X-RAY DIFFRACTION	Local ncs	0.15028	0.05007
13	25	D	X-RAY DIFFRACTION	Local ncs	0.15442	0.05007
13	26	E	X-RAY DIFFRACTION	Local ncs	0.15442	0.05007
14	27	D	X-RAY DIFFRACTION	Local ncs	0.1634	0.05007
14	28	F	X-RAY DIFFRACTION	Local ncs	0.1634	0.05007
15	29	E	X-RAY DIFFRACTION	Local ncs	0.18527	0.05006
15	30	F	X-RAY DIFFRACTION	Local ncs	0.18527	0.05006

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 (%)
2.101-2.156	0.375	207	0.319	3933	X-RAY DIFFRACTION	99.3521
2.156-2.215	0.334	203	0.258	3839	X-RAY DIFFRACTION	99.5566
2.215-2.279	0.321	195	0.225	3721	X-RAY DIFFRACTION	99.6184
2.279-2.349	0.245	191	0.192	3624	X-RAY DIFFRACTION	99.6864
2.349-2.426	0.245	185	0.18	3508	X-RAY DIFFRACTION	99.7838
2.426-2.511	0.238	178	0.182	3384	X-RAY DIFFRACTION	99.8039
2.511-2.606	0.252	172	0.179	3275	X-RAY DIFFRACTION	99.8262
2.606-2.712	0.248	168	0.186	3189	X-RAY DIFFRACTION	99.881
2.712-2.833	0.276	159	0.185	3024	X-RAY DIFFRACTION	99.7806
2.833-2.971	0.25	153	0.194	2899	X-RAY DIFFRACTION	99.8691
2.971-3.131	0.253	143	0.186	2721	X-RAY DIFFRACTION	99.7215
3.131-3.321	0.229	137	0.186	2611	X-RAY DIFFRACTION	99.2058
3.321-3.55	0.224	129	0.181	2452	X-RAY DIFFRACTION	99.8453
3.55-3.834	0.232	120	0.168	2269	X-RAY DIFFRACTION	99.7911
3.834-4.199	0.181	110	0.147	2088	X-RAY DIFFRACTION	99.6825
4.199-4.693	0.141	99	0.133	1894	X-RAY DIFFRACTION	99.4511
4.693-5.417	0.169	88	0.15	1658	X-RAY DIFFRACTION	99.4305
5.417-6.629	0.25	74	0.19	1407	X-RAY DIFFRACTION	99.396
6.629-9.35	0.215	58	0.2	1097	X-RAY DIFFRACTION	99.6549
9.35-45.866	0.231	31	0.195	590	X-RAY DIFFRACTION	98.8854

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