PDB-7b4p: A Bacteroidetes bacterium CuZn-superoxide dismutase with CuZn met...

ID or keywords:

Entry

Database: PDB / ID: 7b4p

Title

A Bacteroidetes bacterium CuZn-superoxide dismutase with CuZn 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: 2.7 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 22, 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 / _atom_site.pdbx_tls_group_id ..._atom_site.calc_flag / _atom_site.pdbx_tls_group_id / _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 6, 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	7b4p.cif.gz	412.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7b4p.ent.gz		Display	PDB format
PDBx/mmJSON format	7b4p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/7b4p ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4p	HTTPS FTP

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Related structure data

Related structure data	7b4oSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7b4p-2 5ax9-2 2pt1-d 6e0o-1 1uu3-d 1fgi-1 1yom-2 3zxz-d 4mcv-1 6bwk-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

65.5 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
32.7 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
32.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.790, 109.593, 122.598
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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: LYS / Beg label comp-ID: LYS

Dom-ID	Component-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	1	ILE	ILE	AAA	A	5 - 151	5 - 151
2	2	1	ILE	ILE	BBB	B	5 - 151	5 - 151
3	3	2	GLY	GLY	AAA	A	5 - 152	5 - 152
4	4	2	GLY	GLY	CCC	C	5 - 152	5 - 152
5	5	3	GLY	GLY	AAA	A	5 - 152	5 - 152
6	6	3	GLY	GLY	DDD	D	5 - 152	5 - 152
7	7	4	ILE	ILE	BBB	B	5 - 151	5 - 151
8	8	4	ILE	ILE	CCC	C	5 - 151	5 - 151
9	9	5	ILE	ILE	BBB	B	5 - 151	5 - 151
10	10	5	ILE	ILE	DDD	D	5 - 151	5 - 151
11	11	6	LYS	LYS	CCC	C	5 - 153	5 - 153
12	12	6	LYS	LYS	DDD	D	5 - 153	5 - 153

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-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.16 Å³/Da / Density % sol: 43.08 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: .12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1- ...Details: .12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 3-(N-morpholino)propane sulfonic acid pH 7.5; 37.5 % precipitant mix containing 2-Methyl-2,4-pentanediol, polyethylene glycol 1000, polyethylene glycol 3350

Crystal

Density Matthews: 2.16 Å³/Da / Density % sol: 43.08 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: .12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1- ...

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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: 2.7→81.71 Å / Num. obs: 16195 / % possible obs: 100 % / Redundancy: 9.2 % / CC_1/2: 0.999 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.7→2.83 Å / Num. unique obs: 2093 / CC_1/2: 0.61

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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: 7B4O

7b4o

Resolution: 2.7→81.7 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.935 / SU B: 43.227 / SU ML: 0.393 / Cross valid method: FREE R-VALUE / ESU R Free: 0.412
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2783	803	4.973 %
R_work	0.2396	15343	-
all	0.242	-	-
obs	-	16146	99.963 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 89.467 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.931 Å²	-0 Å²	0 Å²
2-	-	2.595 Å²	-0 Å²
3-	-	-	-3.526 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→81.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4427	0	8	21	4456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	4511
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4156
X-RAY DIFFRACTION	r_angle_refined_deg	1.213	1.635	6080
X-RAY DIFFRACTION	r_angle_other_deg	1.067	1.594	9659
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.934	5	593
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.359	24.537	205
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.751	15	766
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.934	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.031	0.2	600
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	5219
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	905
X-RAY DIFFRACTION	r_nbd_refined	0.154	0.2	803
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.151	0.2	3863
X-RAY DIFFRACTION	r_nbtor_refined	0.133	0.2	2134
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.064	0.2	2024
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.088	0.2	76
X-RAY DIFFRACTION	r_metal_ion_refined	0.038	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	32
X-RAY DIFFRACTION	r_mcbond_it	0.45	5.841	2384
X-RAY DIFFRACTION	r_mcbond_other	0.45	5.84	2383
X-RAY DIFFRACTION	r_mcangle_it	0.81	8.76	2973
X-RAY DIFFRACTION	r_mcangle_other	0.81	8.76	2974
X-RAY DIFFRACTION	r_scbond_it	0.299	5.874	2127
X-RAY DIFFRACTION	r_scbond_other	0.299	5.874	2127
X-RAY DIFFRACTION	r_scangle_it	0.56	8.796	3107
X-RAY DIFFRACTION	r_scangle_other	0.56	8.796	3107
X-RAY DIFFRACTION	r_lrange_it	3.668	68.424	4531
X-RAY DIFFRACTION	r_lrange_other	3.667	68.428	4532
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	4417
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.045	0.05	4476
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.062	0.05	4448
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.061	0.05	4408
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.064	0.05	4419
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	4457

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	0.06225	0.05011
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.06225	0.05011
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.04528	0.05011
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.04528	0.05011
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06216	0.05011
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06216	0.05011
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.06095	0.05011
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.06095	0.05011
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.06368	0.05011
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.06368	0.05011
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.06448	0.05011
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.06448	0.05011

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 (%)
2.7-2.77	0.439	62	0.425	1108	X-RAY DIFFRACTION	100
2.77-2.846	0.521	58	0.406	1066	X-RAY DIFFRACTION	99.9111
2.846-2.928	0.349	57	0.356	1064	X-RAY DIFFRACTION	99.9109
2.928-3.019	0.382	53	0.333	1026	X-RAY DIFFRACTION	100
3.019-3.117	0.392	60	0.296	965	X-RAY DIFFRACTION	100
3.117-3.227	0.236	43	0.27	1014	X-RAY DIFFRACTION	100
3.227-3.349	0.262	48	0.27	901	X-RAY DIFFRACTION	99.8947
3.349-3.485	0.277	44	0.263	923	X-RAY DIFFRACTION	100
3.485-3.64	0.284	54	0.246	837	X-RAY DIFFRACTION	100
3.64-3.818	0.297	43	0.244	840	X-RAY DIFFRACTION	100
3.818-4.024	0.195	34	0.225	778	X-RAY DIFFRACTION	99.877
4.024-4.268	0.231	39	0.205	761	X-RAY DIFFRACTION	100
4.268-4.562	0.212	33	0.199	713	X-RAY DIFFRACTION	100
4.562-4.927	0.194	33	0.182	669	X-RAY DIFFRACTION	100
4.927-5.396	0.298	34	0.185	616	X-RAY DIFFRACTION	100
5.396-6.032	0.246	38	0.193	562	X-RAY DIFFRACTION	100
6.032-6.962	0.222	25	0.212	504	X-RAY DIFFRACTION	100
6.962-8.52	0.548	18	0.244	434	X-RAY DIFFRACTION	100
8.52-12.02	0.234	16	0.246	346	X-RAY DIFFRACTION	99.7245
12.02-81.7	0.302	11	0.247	216	X-RAY DIFFRACTION	99.5614

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.3248	-1.3005	0.1198	6.7897	1.3522	2.8711	-0.0742	-0.715	-0.515	0.6722	0.187	0.14	0.3942	-0.3053	-0.1128	0.2909	-0.0033	-0.0296	0.2902	0.0205	0.1066	18.101	-35.733	15.71
2	3.3144	-0.4616	0.6806	6.3609	-0.5792	3.3496	-0.1756	-0.6297	0.8686	0.5825	0.1422	0.006	-0.8179	-0.1162	0.0334	0.3966	0.024	-0.0369	0.28	-0.2638	0.3072	15.149	-10.232	15.627
3	4.7103	1.9546	0.2232	5.9182	-1.0925	3.8999	-0.2132	0.9527	-0.5932	-0.7527	0.302	-0.2319	0.3761	0.3977	-0.0888	0.2945	-0.0216	-0.0022	0.2748	-0.0916	0.0997	32.464	-35.288	45.445
4	3.9756	0.2935	1.1343	5.8956	0.9061	5.1548	-0.494	0.8118	0.9705	-0.882	0.3649	0.1716	-1.2	0.4041	0.1291	0.5896	-0.2013	-0.1546	0.2559	0.2721	0.3218	35.439	-9.775	45.949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	5 - 153
2	X-RAY DIFFRACTION	2	ALL	BBB	5 - 152
3	X-RAY DIFFRACTION	3	ALL	CCC	5 - 153
4	X-RAY DIFFRACTION	4	ALL	DDD	5 - 153

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