PDB-9gsk: CSP1 H36A plus imidazole

ID or keywords:

Entry

Database: PDB / ID: 9gsk

Title

CSP1 H36A plus imidazole

Components

Copper storage protein 1

Keywords

METAL BINDING PROTEIN / COPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE

Function / homology

Twin-arginine translocation signal, Cys-rich four helix bundle protein / metal ion binding / COPPER (II) ION / COPPER (I) ION / IMIDAZOLE / Copper storage protein 1

Function and homology information

Biological species

Methylosinus trichosporium OB3b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 1.3 Å

Authors

Basle, A. / David, S. / Dennison, C.

Funding support

1items

Citation

Journal: To Be Published
Title: The replacement of a Met ligand by iodide in a copper storage protein is stabilised by an unusual Cu(I)2-anion-pi interaction
Authors: David, S. / Dalton, R.A. / Basle, A. / Crowley, P.B. / Dennison, C.

History

Deposition	Sep 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gsk.cif.gz	60.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9gsk.ent.gz	41.5 KB	Display	PDB format
PDBx/mmJSON format	9gsk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9gsk_validation.pdf.gz	18.9 MB	Display	wwPDB validaton report
Full document	9gsk_full_validation.pdf.gz	18.8 MB	Display
Data in XML	9gsk_validation.xml.gz	13.6 KB	Display
Data in CIF	9gsk_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gs/9gsk ftp://data.pdbj.org/pub/pdb/validation_reports/gs/9gsk	HTTPS FTP

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Related structure data

Related structure data	8r4lC 8r4mC 9gq1C 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	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Copper storage protein 1

B: Copper storage protein 1

hetero molecules

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

1

A: Copper storage protein 1

B: Copper storage protein 1

hetero molecules

A: Copper storage protein 1

B: Copper storage protein 1

hetero molecules

defined by author&software
48.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.42, 98.28, 83.43
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-1014- CU
2	1	A-1155- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 13 - 122 / Label seq-ID: 1 - 110

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Copper storage protein 1 Mass: 11254.065 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria) Production host: Methylosinus trichosporium OB3b (bacteria) / References: UniProt: A0A0M3KL60
#2: Chemical	... ChemComp-CU1 / COPPER (I) ION Mass: 63.546 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.23 %
Crystal grow	Temperature: 293.5 K / Method: vapor diffusion, sitting drop Details: 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM LFucose, 20 mM D-Xylose, 20 mM N-Acetyl-D-Glucosamine, 100 mM Imidazol/MES pH 6.5, 40% Glycerol and 20% PEG 400.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.3→51.47 Å / Num. obs: 61289 / % possible obs: 100 % / Redundancy: 12.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.024 / R_rim(I) all: 0.062 / Χ²: 0.87 / Net I/σ(I): 16.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
7.12-51.47	10.1	0.028	44.2	432	0.998	0.012	0.031	0.44	99.6
1.3-1.32	13.1	2.232	1.2	3001	0.486	0.931	2.42	0.89	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement

Refinement

Method to determine structure:

MIR / Resolution: 1.3→51.47 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.973 / SU B: 0.789 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.042 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.1806	3118	5.09 %
R_work	0.1709	58139	-
all	0.171	-	-
obs	-	61257	99.982 %

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: 23.281 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.893 Å²	0 Å²	-0 Å²
2-	-	-0.427 Å²	0 Å²
3-	-	-	-0.466 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→51.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1546	0	37	122	1705

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	1647
X-RAY DIFFRACTION	r_angle_refined_deg	2.151	1.808	2231
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.293	5	238
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.948	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.599	10	275
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.64	10	55
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	258
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1228
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	854
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1151
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.096	0.2	86
X-RAY DIFFRACTION	r_metal_ion_refined	0.217	0.2	58
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.251	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	0.2	14
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.194	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.989	2.043	901
X-RAY DIFFRACTION	r_mcangle_it	2.697	3.664	1129
X-RAY DIFFRACTION	r_scbond_it	3.757	2.428	746
X-RAY DIFFRACTION	r_scangle_it	5.294	4.275	1093
X-RAY DIFFRACTION	r_lrange_it	4.986	24.469	2696
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.068	0.05	3367

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	0.06799	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06799	0.05008

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
1.3-1.334	0.326	219	0.302	4265	0.303	4485	0.92	0.928	99.9777	0.294
1.334-1.37	0.289	239	0.28	4154	0.281	4395	0.937	0.941	99.9545	0.267
1.37-1.41	0.264	225	0.259	4026	0.26	4253	0.957	0.954	99.953	0.241
1.41-1.453	0.23	217	0.229	3883	0.229	4100	0.966	0.965	100	0.206
1.453-1.501	0.209	207	0.202	3789	0.202	3996	0.974	0.974	100	0.179
1.501-1.554	0.201	198	0.178	3697	0.179	3895	0.973	0.98	100	0.155
1.554-1.612	0.158	200	0.156	3558	0.156	3758	0.982	0.985	100	0.133
1.612-1.678	0.172	188	0.149	3403	0.15	3591	0.983	0.986	100	0.126
1.678-1.752	0.17	186	0.139	3289	0.141	3475	0.984	0.988	100	0.119
1.752-1.838	0.187	136	0.141	3167	0.143	3303	0.979	0.988	100	0.125
1.838-1.937	0.175	168	0.154	3008	0.155	3176	0.982	0.985	100	0.14
1.937-2.055	0.182	129	0.162	2871	0.163	3000	0.978	0.984	100	0.156
2.055-2.196	0.184	127	0.163	2693	0.164	2820	0.979	0.984	100	0.162
2.196-2.372	0.159	157	0.151	2466	0.152	2625	0.983	0.986	99.9238	0.158
2.372-2.598	0.162	123	0.167	2319	0.167	2442	0.982	0.983	100	0.18
2.598-2.903	0.224	106	0.19	2099	0.191	2205	0.973	0.979	100	0.212
2.903-3.351	0.184	107	0.179	1860	0.179	1967	0.979	0.98	100	0.209
3.351-4.099	0.146	68	0.161	1616	0.161	1684	0.986	0.985	100	0.194
4.099-5.779	0.188	80	0.163	1235	0.164	1315	0.98	0.984	100	0.205
5.779-51.47	0.127	38	0.164	741	0.163	783	0.99	0.979	99.4891	0.217

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