PDB-8bwv: Crystal Structure of SilF Cu(I)

ID or keywords:

Entry

Database: PDB / ID: 8bwv

Title

Crystal Structure of SilF Cu(I)

Components

(SilF) x 2

Keywords

METAL BINDING PROTEIN / Cu(I) Metallochaperone / metal binding

Function / homology

Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / metal ion binding / COPPER (II) ION / SilF

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Lithgo, R.M. / Carr, S.B. / Scott, D.J. / Quigley, A.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: SilF structure with Ag(I) and Cu(I)
Authors: Lithgo, R.M.

History

Deposition	Dec 7, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bwv.cif.gz	107.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8bwv.ent.gz	79.7 KB	Display	PDB format
PDBx/mmJSON format	8bwv.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/bw/8bwv ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwv	HTTPS FTP

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Related structure data

Related structure data	8bbz 8bhu
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

Deposited unit

A: SilF

B: SilF

C: SilF

D: SilF

E: SilF

F: SilF

hetero molecules

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

1

A: SilF

hetero molecules

D: SilF

hetero molecules

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

2

B: SilF

C: SilF

hetero molecules

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

3

E: SilF

F: SilF

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.297, 77.297, 187.690
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	11 - 88
2	1	1	A	11 - 88
3	2	2	A	11 - 89
4	2	2	A	11 - 89
5	3	3	A	11 - 88
6	3	3	A	11 - 88
7	4	4	A	11 - 88
8	4	4	A	11 - 88
9	5	5	A	11 - 88
10	5	5	A	11 - 88
11	6	6	A	11 - 88
12	6	6	A	11 - 88
13	7	7	A	11 - 90
14	7	7	A	11 - 90
15	8	8	A	11 - 90
16	8	8	A	11 - 90
17	9	9	A	11 - 90
18	9	9	A	11 - 90
19	10	10	A	11 - 88
20	10	10	A	11 - 88
21	11	11	A	11 - 88
22	11	11	A	11 - 88
23	12	12	A	11 - 88
24	12	12	A	11 - 88
25	13	13	A	11 - 90
26	13	13	A	11 - 90
27	14	14	A	11 - 90
28	14	14	A	11 - 90
29	15	15	A	11 - 90
30	15	15	A	11 - 90

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	SilF Mass: 8595.927 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482M8M0
#2: Protein	SilF Mass: 8695.058 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482M8M0
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.7 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium sodium tartrate tetrahydrate & 20% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2.2→47.275 Å / Num. obs: 28978 / % possible obs: 99.9 % / Redundancy: 24.2 % / B_iso Wilson estimate: 43.13 Å² / CC_1/2: 0.997 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.2→2.2 Å / Redundancy: 16.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2855 / CC_1/2: 0.901 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→47.275 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.94 / SU B: 9.025 / SU ML: 0.212 / Cross valid method: FREE R-VALUE / ESU R: 0.333 / ESU R Free: 0.243
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2986	1427	4.924 %
R_work	0.2797	27551	-
all	0.281	-	-
obs	-	28978	99.91 %

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: 55.098 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.136 Å²	0 Å²	-0 Å²
2-	-	0.047 Å²	0 Å²
3-	-	-	-0.183 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→47.275 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3634	0	12	9	3655

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3688
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3660
X-RAY DIFFRACTION	r_angle_refined_deg	1.44	1.62	4984
X-RAY DIFFRACTION	r_angle_other_deg	0.502	1.574	8384
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.783	5	472
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.036	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.247	10	658
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.509	10	150
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	596
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4252
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	820
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	658
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	3352
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1805
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2079
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	65
X-RAY DIFFRACTION	r_metal_ion_refined	0.219	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.317	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	173
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.147	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	5.34	5.096	1906
X-RAY DIFFRACTION	r_mcbond_other	5.334	5.096	1906
X-RAY DIFFRACTION	r_mcangle_it	8.094	9.127	2372
X-RAY DIFFRACTION	r_mcangle_other	8.094	9.13	2373
X-RAY DIFFRACTION	r_scbond_it	6.238	5.763	1782
X-RAY DIFFRACTION	r_scbond_other	6.236	5.766	1783
X-RAY DIFFRACTION	r_scangle_it	9.57	10.349	2612
X-RAY DIFFRACTION	r_scangle_other	9.568	10.352	2613
X-RAY DIFFRACTION	r_lrange_it	11.526	48.81	3883
X-RAY DIFFRACTION	r_lrange_other	11.525	48.823	3884
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.127	0.05	2128
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.071	0.05	2272
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.108	0.05	2143
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.104	0.05	2184
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.109	0.05	2166
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.124	0.05	2121
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.08	0.05	2320
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.112	0.05	2255
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.107	0.05	2253
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.116	0.05	2115
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.111	0.05	2160
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.106	0.05	2163
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.099	0.05	2266
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.088	0.05	2257
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.078	0.05	2323

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	0.12673	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12673	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07105	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07105	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10791	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10791	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.10373	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.10373	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.1092	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.1092	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12368	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12368	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08029	0.05011
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08029	0.05011
8	15	A	X-RAY DIFFRACTION	Local ncs	0.11211	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.11211	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.10686	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.10686	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.11649	0.05008
10	20	A	X-RAY DIFFRACTION	Local ncs	0.11649	0.05008
11	21	A	X-RAY DIFFRACTION	Local ncs	0.11073	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.11073	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.10593	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.10593	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.09927	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.09927	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.0879	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.0879	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.07842	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.07842	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.2-2.257	0.466	101	0.401	2003	0.404	2105	0.841	0.893	99.9525	0.378
2.257-2.319	0.382	108	0.41	1929	0.408	2038	0.897	0.896	99.9509	0.389
2.319-2.386	0.367	111	0.388	1903	0.387	2015	0.899	0.9	99.9504	0.364
2.386-2.459	0.451	80	0.376	1839	0.379	1920	0.875	0.911	99.9479	0.343
2.459-2.54	0.341	105	0.343	1817	0.343	1924	0.92	0.929	99.896	0.316
2.54-2.628	0.37	114	0.318	1706	0.321	1823	0.921	0.941	99.8354	0.294
2.628-2.727	0.307	102	0.311	1642	0.311	1745	0.944	0.944	99.9427	0.285
2.727-2.838	0.265	84	0.302	1628	0.301	1713	0.972	0.948	99.9416	0.28
2.838-2.964	0.331	93	0.3	1553	0.302	1648	0.944	0.947	99.8786	0.289
2.964-3.108	0.364	68	0.321	1514	0.323	1582	0.896	0.936	100	0.307
3.108-3.275	0.33	82	0.311	1404	0.312	1486	0.943	0.943	100	0.304
3.275-3.473	0.347	79	0.31	1321	0.312	1400	0.932	0.947	100	0.309
3.473-3.711	0.268	56	0.281	1288	0.28	1345	0.962	0.958	99.9257	0.28
3.711-4.007	0.244	44	0.285	1209	0.283	1253	0.975	0.957	100	0.291
4.007-4.386	0.226	39	0.222	1121	0.222	1161	0.975	0.975	99.9139	0.235
4.386-4.898	0.233	44	0.203	1007	0.204	1052	0.971	0.978	99.9049	0.225
4.898-5.646	0.168	34	0.184	901	0.183	936	0.99	0.984	99.8932	0.201
5.646-6.89	0.235	32	0.241	775	0.241	807	0.976	0.974	100	0.259
6.89-9.643	0.182	27	0.203	622	0.202	649	0.992	0.979	100	0.228
9.643-47.275	0.321	24	0.308	371	0.309	396	0.951	0.937	99.7475	0.352

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