PDB-4r9x: Crystal Structure of Putative Copper Homeostasis Protein CutC fro...

ID or keywords:

Entry

Database: PDB / ID: 4r9x

Title

Crystal Structure of Putative Copper Homeostasis Protein CutC from Bacillus anthracis

Components

Copper homeostasis protein CutC

Keywords

METAL TRANSPORT /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold /

TIM barrel

Function / homology

Function and homology information

intracellular copper ion homeostasis / copper ion binding /

cytoplasm
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8515 Å

Authors

Kim, Y. / Zhou, M. / Makowska-Grzyska, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published / Year: 2014
Title: Crystal Structure of Putative Copper Homeostasis Protein CutC from Bacillus anthracis
Authors: Kim, Y. / Zhou, M. / Makowska-Grzyska, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / CSGID

History

Deposition	Sep 8, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Database references / Structure summary
Revision 1.2	Jan 24, 2018	Group: Data collection / Structure summary / Category: audit_author / diffrn_radiation Item: _audit_author.name / _diffrn_radiation.pdbx_diffrn_protocol

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4r9x.cif.gz	188.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4r9x.ent.gz	160.2 KB	Display	PDB format
PDBx/mmJSON format	4r9x.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/r9/4r9x ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r9x	HTTPS FTP

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Related structure data

Similar structure data	5xni-1 6czd-1 3g7p-1 4jc2-3 4yos-d 4wop-2 7byx-3 2xvm-d 6nl5-1 6nl5-2 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
Other databases	TargetTrack: CSGID-IDP04109

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Copper homeostasis protein CutC

B: Copper homeostasis protein CutC

hetero molecules

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

1

A: Copper homeostasis protein CutC

hetero molecules

B: Copper homeostasis protein CutC

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.335, 58.335, 118.967
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Copper homeostasis protein CutC / Putative copper homeostasis protein CutC Mass: 25915.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS2885, BA_3100, cutC, GBAA_3100 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q81NS5, UniProt: A0A6L8Q3J2*PLUS

#1: Protein

Copper homeostasis protein CutC / Putative copper homeostasis protein CutC

Mass: 25915.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS2885, BA_3100, cutC, GBAA_3100 / Plasmid: pMCSG28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q81NS5, UniProt: A0A6L8Q3J2*PLUS

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Non-polymers , 5 types, 170 molecules

#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.45 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Calcium acetate, 0.1 M sodium cacodylate pH 6.5, 40 %(w/v) PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97905 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 16, 2014 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97905 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. all: 38473 / Num. obs: 38473 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / B_iso Wilson estimate: 15.98 Å² / R_sym value: 0.059 / Net I/σ(I): 24.7
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.31 / Num. unique all: 1990 / R_sym value: 0.642 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
DM		model building
PHENIX	(phenix.refine: dev_1745)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8515→28.329 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.206	1890	5.04 %	random
R_work	0.176	-	-	-
all	0.177	37508	-	-
obs	0.177	37508	97.08 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 27.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.8515→28.329 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3458	0	23	164	3645

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3591
X-RAY DIFFRACTION	f_angle_d	1.218	4853
X-RAY DIFFRACTION	f_dihedral_angle_d	16.43	1372
X-RAY DIFFRACTION	f_chiral_restr	0.056	586
X-RAY DIFFRACTION	f_plane_restr	0.006	626

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.8515-1.9015	0.2275	128	0.2086	2376	2504	79
1.9015-1.9573	0.2184	151	0.2042	2686	2837	91
1.9573-2.0204	0.2576	137	0.2057	2828	2965	95
2.0204-2.0925	0.2384	163	0.2059	2792	2955	94
2.0925-2.1762	0.2051	138	0.1956	2795	2933	94
2.1762-2.275	0.2272	142	0.1937	2761	2903	94
2.275-2.3946	0.2236	134	0.1904	2781	2915	94
2.3946-2.5442	0.248	146	0.1967	2795	2941	93
2.5442-2.74	0.2827	154	0.2065	2730	2884	93
2.74-3.0144	0.2033	155	0.1967	2777	2932	94
3.0144-3.4476	0.1803	143	0.1742	2809	2952	94
3.4476-4.3323	0.1646	144	0.1319	2723	2867	93
4.3323-17.3204	0.1811	137	0.1419	2734	2871	92

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	1.9634	-0.2331	0.8036	0.8808	0.2016	1.4613	0.1029	-0.0576	-0.1308	-0.0629	0.0261	0.2252	-0.0717	-0.369	-0.1236	0.0907	0.0271	-0.0054	0.1824	0.0119	0.1391	16.0073	14.4634	31.5077
2	2.637	0.3264	0.003	3.8389	-1.5639	7.1154	0.0615	-0.2288	0.0043	-0.0302	-0.0632	-0.0422	-0.1286	-0.0528	0.0392	0.156	0.0416	0.0104	0.1584	-0.0147	0.0575	26.8083	17.8271	44.101
3	1.1235	0.8147	-0.8087	3.1394	-0.3322	3.1789	-0.0608	-0.5833	-0.2439	0.5246	-0.2381	0.0978	-0.0492	-0.0463	0.2281	0.1933	0.0396	0.0472	0.3356	0.0646	0.1686	15.9717	14.2471	48.8752
4	1.9352	0.43	0.3896	0.5844	0.0273	1.0393	0.0153	-0.5202	-0.1748	0.2206	0.0913	0.3148	-0.1113	-0.6537	-0.0126	0.1702	0.0919	0.066	0.4514	0.0618	0.2556	9.6788	15.5107	48.5553
5	2.0325	0.786	0.4091	1.197	-0.4486	0.4944	0.0212	-0.5332	-0.1032	0.3098	0.0789	0.4681	-0.0317	-0.2969	-0.0432	0.1465	0.0753	0.0563	0.5931	0.125	0.4518	-1.3181	13.5716	43.1078
6	0.8601	0.1891	0.1417	0.2241	0.1454	0.3752	-0.0815	-0.1895	-0.0288	0.0612	0.0794	0.2274	0.0452	-0.236	0.047	0.0942	0.0097	-0.0245	0.4733	0.1162	0.4377	-2.0678	12.1164	35.4157
7	1.5519	-1.9888	0.3513	3.6953	-1.5233	1.0837	0.1941	0.1635	-0.4257	-0.1182	0.0841	0.0727	0.5524	-0.3834	-0.2722	0.236	-0.0285	-0.1156	0.2535	-0.0279	0.415	10.2048	4.1144	22.884
8	2.9467	-0.1725	-3.6656	0.3299	0.1918	4.5607	0.1058	0.324	0.0371	-0.1386	0.0011	0.4103	-0.3464	-0.4605	-0.0921	0.1602	0.0305	-0.0733	0.5085	0.05	0.3396	-1.5132	13.9272	23.7785
9	1.3192	-0.5303	0.3842	1.2143	-0.6137	1.3548	0.1008	0.0027	-0.1962	-0.0265	-0.0348	0.0044	0.3281	0.3564	-0.0807	0.1426	0.0617	-0.0202	0.1846	0.0053	0.13	4.5905	54.7692	36.1999
10	2.2588	0.0215	2.0773	0.8019	-0.3621	3.5338	-0.0095	0.1504	-0.001	-0.0267	-0.0232	0.0043	-0.0206	0.3324	0.0458	0.0987	0.0159	0.0185	0.1773	0.0077	0.0795	2.3906	65.8586	24.283
11	1.6712	0.4984	-0.2369	1.929	0.6777	2.0935	0.0823	0.2178	-0.2166	-0.5653	-0.0829	0.192	-0.0442	0.1662	-0.0429	0.3193	0.1579	-0.067	0.2494	-0.1083	0.1982	3.4623	53.6108	18.0758
12	0.8463	0.2545	0.044	1.1	-0.3351	0.5345	0.0946	0.341	-0.3552	-0.3489	0.0315	-0.1819	0.4918	0.5521	-0.1152	0.368	0.1946	-0.0364	0.3698	-0.0904	0.1785	8.5996	52.1537	17.345
13	1.7798	-1.1939	0.047	2.2928	0.0314	0.9878	0.1709	0.1154	-0.2728	-0.1455	0.0184	0.1984	0.2826	0.1503	0.1132	0.3128	0.2379	-0.0746	0.2908	-0.1008	0.2739	9.117	45.8989	22.617
14	0.0045	-0.0544	-0.027	0.8929	0.0742	0.2836	0.0119	0.2405	-0.4438	-0.1539	0.01	-0.1837	0.2561	0.1683	0.029	0.4385	0.2208	-0.0675	0.3328	-0.1352	0.4816	13.8894	40.1491	21.0637
15	0.9624	-0.9155	-0.4493	0.8802	0.4803	0.4907	-0.1097	-0.0633	-0.3271	0.1223	0.0718	0.1466	0.1549	0.0723	0.1087	0.5002	0.2635	-0.1184	0.2646	-0.0898	0.5621	10.5566	33.7121	32.8502
16	1.5284	-0.0949	-0.2764	2.1413	0.2664	1.2572	0.0415	-0.077	-0.4101	0.2134	-0.0261	-0.02	0.3129	0.1269	-0.0278	0.3142	0.099	-0.0866	0.188	0.0082	0.3125	5.9677	41.9903	37.4147
17	3.0688	-1.0437	-1.3384	1.9341	-0.0086	2.4217	-0.0816	-0.4398	-0.4751	0.3869	0.2087	-0.0486	0.4884	0.2746	-0.1041	0.4392	0.1043	-0.0861	0.2662	0.053	0.271	7.529	41.5985	44.3407

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 156 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 157 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 202 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 203 through 213 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 214 through 225 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 83 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 84 through 100 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 101 through 137 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 138 through 154 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 155 through 176 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 177 through 191 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 192 through 206 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 207 through 225 )

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