PDB-7b4o: A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn met...

ID or keywords:

Entry

Database: PDB / ID: 7b4o

Title

A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn metalation

Components

Superoxide dismutase [Cu-Zn]

Keywords

OXIDOREDUCTASE / Superoxide dismutase / copper / zinc / bacterial

Function / homology

Function and homology information

superoxide dismutase / superoxide dismutase activity / copper ion binding
Similarity search - Function

Biological species

Bacteroidetes bacterium GWA2_30_7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.41 Å

Authors

Wright, G.S.A.

Funding support

United Kingdom, 1items

Citation

Journal: Mol.Biol.Evol. / Year: 2021
Title: Bacterial Evolutionary Precursors of Eukaryotic Copper-Zinc Superoxide Dismutases.
Authors: Wright, G.S.A.

History

Deposition	Dec 2, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 2, 2021	Provider: repository / Type: Initial release
Revision 2.0	Sep 29, 2021	Group: Atomic model / Data collection / Database references Category: atom_site / citation ...atom_site / citation / database_2 / pdbx_database_proc Item: _atom_site.calc_flag / _citation.journal_volume ..._atom_site.calc_flag / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2	Nov 20, 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	7b4o.cif.gz	433.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7b4o_validation.pdf.gz	441.9 KB	Display	wwPDB validaton report
Full document	7b4o_full_validation.pdf.gz	443.1 KB	Display
Data in XML	7b4o_validation.xml.gz	28.2 KB	Display
Data in CIF	7b4o_validation.cif.gz	41.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/7b4o ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4o	HTTPS FTP

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Related structure data

Related structure data	7b4pC 2c9vS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7b4o-2 7b4p-2 7a2a-1 4cqe-2 6h1u-d 4m67-d 7b4p-1 6e0o-1 6z4b-1 3cfz-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	#94 - Oct 2007 Superoxide Dismutase similarity (9)

Deposited unit

AAA: Superoxide dismutase [Cu-Zn]

BBB: Superoxide dismutase [Cu-Zn]

CCC: Superoxide dismutase [Cu-Zn]

DDD: Superoxide dismutase [Cu-Zn]

hetero molecules

65.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Superoxide dismutase [Cu-Zn]

BBB: Superoxide dismutase [Cu-Zn]

hetero molecules

defined by author&software
Evidence: gel filtration
33 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: Superoxide dismutase [Cu-Zn]

DDD: Superoxide dismutase [Cu-Zn]

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.469, 96.637, 136.118
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	AAA-203- ZN
2	1	AAA-465- HOH
3	1	DDD-465- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 4 - 153 / Label seq-ID: 4 - 153

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	2	1	BBB	B
3	3	2	AAA	A
4	4	2	CCC	C
5	5	3	AAA	A
6	6	3	DDD	D
7	7	4	BBB	B
8	8	4	CCC	C
9	9	5	BBB	B
10	10	5	DDD	D
11	11	6	CCC	C
12	12	6	DDD	D

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

#1: Protein	Superoxide dismutase [Cu-Zn] Mass: 16240.186 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroidetes bacterium GWA2_30_7 (bacteria) Gene: A2046_17220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1F3DVA5, superoxide dismutase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.44 Å³/Da / Density % sol: 49.63 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM tris(hydroxymethyl)aminomethane-HCl, 20 % polyethylene glycol 6000, 2 mM ZnCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.41→68.27 Å / Num. obs: 122059 / % possible obs: 100 % / Redundancy: 7.5 % / CC_1/2: 0.998 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.41→1.43 Å / Num. unique obs: 5982 / CC_1/2: 0.345

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2c9v

2c9v

Resolution: 1.41→68.27 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.347 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1918	6227	5.104 %
R_work	0.1589	115779	-
all	0.161	-	-
obs	-	122006	99.974 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 19.872 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.371 Å²	0 Å²	-0 Å²
2-	-	-3.167 Å²	0 Å²
3-	-	-	0.795 Å²

Refinement step

Cycle: LAST / Resolution: 1.41→68.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4440	0	15	564	5019

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	4663
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4277
X-RAY DIFFRACTION	r_angle_refined_deg	1.358	1.636	6313
X-RAY DIFFRACTION	r_angle_other_deg	1.384	1.594	9966
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.868	5	632
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.22	24.673	214
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.244	15	797
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.742	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	621
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5481
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	943
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	882
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	4123
X-RAY DIFFRACTION	r_nbtor_refined	0.147	0.2	2239
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	2110
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	491
X-RAY DIFFRACTION	r_metal_ion_refined	0.078	0.2	22
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.214	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	0.2	28
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.169	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.534	1.733	2459
X-RAY DIFFRACTION	r_mcbond_other	1.534	1.732	2458
X-RAY DIFFRACTION	r_mcangle_it	2.101	2.609	3087
X-RAY DIFFRACTION	r_mcangle_other	2.101	2.61	3088
X-RAY DIFFRACTION	r_scbond_it	7.662	2.237	2202
X-RAY DIFFRACTION	r_scbond_other	7.661	2.237	2202
X-RAY DIFFRACTION	r_scangle_it	9.102	3.13	3217
X-RAY DIFFRACTION	r_scangle_other	9.102	3.131	3217
X-RAY DIFFRACTION	r_lrange_it	6.688	23.324	5192
X-RAY DIFFRACTION	r_lrange_other	6.558	22.523	5022
X-RAY DIFFRACTION	r_rigid_bond_restr	8.217	3	8938
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.092	0.05	4519
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.099	0.05	4485
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.063	0.05	4645
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.05	0.05	4764
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.085	0.05	4629
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.097	0.05	4570

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.09226	0.0501
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.09226	0.0501
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.09935	0.0501
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.09935	0.0501
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06271	0.05011
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06271	0.05011
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.05043	0.05011
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.05043	0.05011
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.08455	0.0501
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.08455	0.0501
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.09711	0.0501
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09711	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 (%)
1.41-1.447	0.299	466	0.31	8488	X-RAY DIFFRACTION	100
1.447-1.486	0.321	432	0.286	8307	X-RAY DIFFRACTION	100
1.486-1.529	0.27	469	0.262	8023	X-RAY DIFFRACTION	99.9882
1.529-1.576	0.247	471	0.223	7774	X-RAY DIFFRACTION	100
1.576-1.628	0.228	386	0.193	7605	X-RAY DIFFRACTION	99.9875
1.628-1.685	0.213	391	0.165	7342	X-RAY DIFFRACTION	100
1.685-1.749	0.19	375	0.155	7149	X-RAY DIFFRACTION	100
1.749-1.82	0.181	346	0.138	6806	X-RAY DIFFRACTION	100
1.82-1.901	0.176	358	0.133	6578	X-RAY DIFFRACTION	100
1.901-1.994	0.17	351	0.135	6233	X-RAY DIFFRACTION	100
1.994-2.102	0.161	285	0.135	6028	X-RAY DIFFRACTION	100
2.102-2.229	0.176	331	0.132	5635	X-RAY DIFFRACTION	99.9497
2.229-2.383	0.172	277	0.124	5370	X-RAY DIFFRACTION	99.9646
2.383-2.574	0.171	272	0.126	4940	X-RAY DIFFRACTION	100
2.574-2.82	0.177	215	0.142	4625	X-RAY DIFFRACTION	100
2.82-3.152	0.175	245	0.145	4150	X-RAY DIFFRACTION	99.9773
3.152-3.64	0.172	195	0.157	3698	X-RAY DIFFRACTION	99.9487
3.64-4.457	0.188	171	0.147	3127	X-RAY DIFFRACTION	99.8184
4.457-6.299	0.195	120	0.164	2475	X-RAY DIFFRACTION	99.7693
6.299-68.27	0.222	71	0.215	1426	X-RAY DIFFRACTION	99.3364

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