PDB-4hci: Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 from ...

ID or keywords:

Entry

Database: PDB / ID: 4hci

Title

Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 from Bacillus anthracis

Components

Cupredoxin 1

Keywords

OXIDOREDUCTASE /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID /

beta-sandwich / greek-key beta-barrel

Function / homology

Function and homology information

copper ion binding /

metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.63 Å

Authors

Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Uncharacterized Cupredoxin-like Domain Protein Cupredoxin_1 from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hci.cif.gz	85.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4hci.ent.gz	70.7 KB	Display	PDB format
PDBx/mmJSON format	4hci.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/hc/4hci ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hci	HTTPS FTP

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Related structure data

Related structure data	4hcf 4hcg
Similar structure data	4hcf-1 5tk2-3 5tk2-4 3hi9-3 3a2e-2 5tk2-1 3lbk-d 5lxl-d 5tk2-2 3s8w-2 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
Other databases	TargetTrack: CSGID-IDP05418

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cupredoxin 1

B: Cupredoxin 1

hetero molecules

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

1

A: Cupredoxin 1

hetero molecules

defined by software
11.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cupredoxin 1

defined by software
11.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.200, 42.809, 51.245
Angle α, β, γ (deg.)	90.00, 120.40, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-257- HOH

#1: Protein	Cupredoxin 1 Mass: 11088.687 Da / Num. of mol.: 2 / Fragment: UNP residues 33-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_1561, GBAA_1561 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81ST4, UniProt: A0A6L7H6L8*PLUS
#2: 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
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.03 Å³/Da / Density % sol: 39.43 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.86 M ammonium nitrate, 150 mM Tris pH 8.0, 100 mM sodium iodide, 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: 0.97926 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 13, 2012 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.63→50 Å / Num. all: 21617 / Num. obs: 21617 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / R_sym value: 0.077 / Net I/σ(I): 19.9
Reflection shell	Resolution: 1.63→1.66 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.508 / Num. unique all: 1008 / R_sym value: 0.029 / % possible all: 93.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
RESOLVE		model building
SOLVE		phasing
PHENIX	(phenix.refine: 1.8.1_1161)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.63→24.521 Å / SU ML: 0.15 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.202	1095	5.11 %	random
R_work	0.178	-	-	-
all	0.179	21417	-	-
obs	0.179	21417	95.61 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.63→24.521 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1405	0	6	115	1526

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1477
X-RAY DIFFRACTION	f_angle_d	1.132	1995
X-RAY DIFFRACTION	f_dihedral_angle_d	15.053	577
X-RAY DIFFRACTION	f_chiral_restr	0.075	241
X-RAY DIFFRACTION	f_plane_restr	0.005	247

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 (%)
1.6296-1.7037	0.3018	126	0.2872	2375	2501	91
1.7037-1.7935	0.2861	129	0.2465	2553	2682	96
1.7935-1.9059	0.257	120	0.2169	2554	2674	96
1.9059-2.0529	0.2037	139	0.1957	2572	2711	97
2.0529-2.2594	0.2291	145	0.1926	2569	2714	97
2.2594-2.586	0.2283	141	0.1981	2588	2729	98
2.586-3.2569	0.1964	152	0.182	2600	2752	97
3.2569-24.5237	0.175	143	0.1479	2511	2654	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	6.1831	0.5575	0.882	5.0706	0.035	5.8353	-0.6617	0.8967	-0.1014	-0.7428	0.4956	-0.6839	0.4566	0.6942	-0.0406	0.4083	0.066	0.0248	0.3483	-0.0596	0.3395	25.0318	14.4892	-2.9435
2	4.0696	0.4502	2.1314	3.7977	-0.3922	4.8058	0.3627	0.7472	-0.63	0.2023	-0.293	-0.0207	1.702	0.0245	-0.1298	0.5301	-0.0416	-0.0015	0.3648	-0.0597	0.276	15.1358	10.1617	-0.8672
3	3.9399	-0.493	0.9453	3.4076	-0.2073	4.897	0.2539	-0.317	-0.7304	-0.0371	-0.1353	-0.6989	1.4773	0.1646	-0.0698	0.375	0.1544	0.0204	0.2929	-0.0909	0.3527	27.3581	12.6698	6.2563
4	5.8373	-0.0045	1.2222	4.3515	-0.9496	6.4552	-0.1075	0.6092	-0.2183	-0.0651	0.0804	-0.9934	-0.2112	0.8772	-0.0123	0.3331	0.0312	0.0189	0.3297	0.0127	0.4318	28.9138	20.1848	1.7851
5	2.2757	-1.661	-0.9154	5.9755	1.0371	9.1024	0.2759	1.3223	0.1924	-0.3392	-0.3231	0.1871	0.2937	-1.3572	0.1288	0.5035	-0.0376	-0.0379	0.5685	-0.0291	0.2756	11.0522	15.6334	-7.0999
6	4.6271	0.0746	2.1271	3.4585	1.3773	6.881	-0.1456	-0.0876	0.1861	-0.149	0.0286	0.0865	-0.3035	-0.4196	0.1265	0.2738	0.0108	0.0206	0.2274	0.0079	0.2062	17.9101	21.9784	5.7125
7	6.416	1.491	3.2324	3.1523	1.7249	7.0854	-0.23	0.73	0.9156	-0.587	-0.0621	-0.0568	0.011	0.1912	0.1286	0.418	0.0385	0.0461	0.4034	0.0741	0.3467	21.1158	22.6663	-4.9312
8	4.9578	0.114	0.291	4.1485	-1.2036	4.9379	-0.2576	-0.6501	-0.2592	0.5539	0.089	-0.7051	-0.0572	0.2421	0.1505	0.4194	0.0659	-0.0821	0.3368	-0.0179	0.337	24.6676	19.1633	12.6696
9	5.4185	0.8797	-0.0313	7.0222	-0.6959	4.3251	-0.1082	0.4708	-0.08	-0.0724	-0.0894	-0.0029	0.4465	-0.4188	0.0781	0.3643	-0.07	-0.0059	0.3101	-0.0304	0.1963	9.4596	15.463	4.2178
10	6.2269	-2.507	3.7272	1.0456	-1.5333	2.3408	0.4218	-1.1127	-0.7196	0.5092	-0.214	-0.4833	0.846	-0.176	0.1643	0.4066	0.0365	-0.0386	0.3546	-0.0128	0.3209	25.1113	13.3302	11.2395
11	6.3874	4.352	-5.8404	5.5087	-5.4382	6.9053	0.391	-0.5969	0.5791	0.4516	0.0654	0.8007	-0.0965	0.0121	-0.5213	0.3161	0.0608	0.0062	0.4952	0.0373	0.3822	-8.6473	20.3904	24.3386
12	1.9971	0.9395	-0.5425	6.3884	-2.4748	3.1497	0.0353	-0.1495	0.1871	0.5249	0.0727	0.1391	-0.2901	0.0438	-0.0669	0.2076	0.0064	0.0156	0.3242	-0.0066	0.2358	0.6951	20.4438	23.5136
13	3.3454	2.2573	-2.5067	7.9032	-5.2455	4.3503	-0.0563	0.219	0.4106	0.0411	0.3749	0.3808	-0.166	-0.0931	-0.3611	0.2471	-0.0125	-0.0312	0.3746	0.06	0.3479	-4.5135	26.1931	15.249
14	2.3	0.3522	0.1434	6.1806	-2.6922	5.4051	0.1312	0.3105	0.0532	-0.4028	-0.1407	0.0021	0.5359	-0.1755	-0.0607	0.2561	-0.0572	0.0128	0.3223	0.0045	0.2528	2.6673	17.1725	13.0525
15	2.2332	1.4969	-0.6973	4.0051	-4.9437	6.4098	-0.0056	0.2853	0.4606	-0.0966	0.2727	0.4816	-0.4007	-0.326	-0.6478	0.2888	0.0253	-0.0099	0.4964	0.1104	0.3818	-7.6631	22.4564	12.9934
16	0.2272	0.888	-0.6573	5.6151	-3.6279	4.0879	-0.0704	-0.0321	-0.0368	-0.3562	-0.0864	-0.1632	0.2153	0.2443	0.1946	0.2102	0.0204	0.0119	0.2975	-0.0017	0.2511	4.9351	12.1649	21.3111
17	4.308	1.8558	-1.1174	6.1787	-1.4596	5.2433	-0.1246	0.151	0.0724	-0.2995	0.3388	-0.1512	-0.2674	0.0908	-0.0891	0.2301	-0.0219	0.025	0.2545	0.0075	0.2952	8.3462	26.1362	10.7878
18	3.779	2.853	-2.865	3.6079	-4.5031	6.2974	0.0289	-0.5056	-0.3058	0.1893	-0.3662	-0.6417	0.084	0.6109	0.1137	0.2623	-0.0034	-0.0331	0.3338	0.0335	0.3142	5.9327	16.7656	25.0451

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 43 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 73 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 78 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 79 through 92 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 93 through 102 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 103 through 113 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 114 through 122 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 123 through 129 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 38 through 50 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 51 through 66 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 67 through 78 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 79 through 92 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 93 through 102 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 103 through 113 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 114 through 122 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 123 through 129 )

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