PDB-3k6c: Crystal structure of protein ne0167 from nitrosomonas europaea

ID or keywords:

Entry

Database: PDB / ID: 3k6c

Title

Crystal structure of protein ne0167 from nitrosomonas europaea

Components

Uncharacterized protein NE0167

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / unknown function PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS

Function / homology

Helix Hairpins - #1960 / Ferritin-like protein / Helix Hairpins / Ferritin-like / Ferritin-like superfamily / Helix non-globular / Special / Uncharacterized protein

Function and homology information

Biological species

Nitrosomonas europaea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Chang, C. / Evdokimova, E. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Protein Ne0167 from Nitrosomonas Europaea
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Oct 8, 2009	Deposition site: RCSB / Processing site: RCSB
Supersession	Oct 27, 2009	ID: 1ZPY
Revision 1.0	Oct 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3k6c.cif.gz	185.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3k6c.ent.gz	160.1 KB	Display	PDB format
PDBx/mmJSON format	3k6c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3k6c_validation.pdf.gz	499.4 KB	Display	wwPDB validaton report
Full document	3k6c_full_validation.pdf.gz	523.9 KB	Display
Data in XML	3k6c_validation.xml.gz	37.6 KB	Display
Data in CIF	3k6c_validation.cif.gz	53.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/3k6c ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k6c	HTTPS FTP

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Related structure data

Similar structure data	6suw-3 6suw-2 6sv1-3 5l8g-3 5l89-2 6sv1-1 5da5-1 5da5-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC5620

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (2) #35 - Nov 2002 Ferritin and Transferrin similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Uncharacterized protein NE0167

B: Uncharacterized protein NE0167

C: Uncharacterized protein NE0167

D: Uncharacterized protein NE0167

E: Uncharacterized protein NE0167

F: Uncharacterized protein NE0167

G: Uncharacterized protein NE0167

H: Uncharacterized protein NE0167

I: Uncharacterized protein NE0167

J: Uncharacterized protein NE0167

114 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	48.417, 134.551, 78.458
Angle α, β, γ (deg.)	90.00, 96.24, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Uncharacterized protein NE0167 Mass: 11406.338 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / Gene: NE0167 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q82XT5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.3 Å³/Da / Density % sol: 45.1 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: K/NA TARTRATE, PEG3350, PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 / Wavelength: 0.97924 Å
Detector	Type: CUSTOM-MADE / Detector: CCD / Date: Apr 3, 2005
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 50572 / Num. obs: 50559 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / B_iso Wilson estimate: 35.3 Å² / R_merge(I) obs: 0.099 / Net I/σ(I): 26.3
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.735 / Mean I/σ(I) obs: 2.82 / Num. unique all: 4980 / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		model building
RESOLVE		model building
Coot		model building
ARP/wARP		model building
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.91 / SU B: 19.483 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26139	2569	5.1 %	RANDOM
R_work	0.22075	-	-	-
all	0.22291	50511	-	-
obs	0.22291	50511	99.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 6.443 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.9 Å²	0 Å²	-0.15 Å²
2-	-	1.47 Å²	0 Å²
3-	-	-	1.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7567	0	0	344	7911

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	7704
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.622	1.963	10368
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.874	5	899
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.476	24.499	449
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.157	15	1460
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.076	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	1099
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5926
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.668	1.5	4555
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.228	2	7312
X-RAY DIFFRACTION	r_scbond_it	1.941	3	3149
X-RAY DIFFRACTION	r_scangle_it	2.924	4.5	3056
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.199→2.256 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.331	176	-
R_work	0.274	3447	-
obs	-	-	98.53 %

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	4.5635	1.1063	0.5378	1.4658	0.095	0.1986	-0.1473	-0.3809	0.2812	-0.1235	0.1435	0.0355	0.0052	-0.0503	0.0038	0.3613	0.0253	0.0135	0.396	-0.0798	0.27	20.4348	70.6667	34.2601
2	2.0783	-0.2377	-0.699	1.6465	-1.6127	1.8514	0.0106	-1.4328	0.3043	0.2369	0.0942	-0.0809	-0.0847	0.2265	-0.1048	0.3327	-0.0464	-0.005	0.9661	-0.1806	0.1503	26.4958	69.3366	46.9192
3	7.775	2.1882	0.2975	1.96	0.3488	0.509	-0.1121	-0.2624	0.2819	-0.0599	0.1546	0.0115	-0.0386	-0.0474	-0.0426	0.3546	0.0339	0.0268	0.3816	0.0065	0.2217	29.0568	64.6718	33.276
4	1.7085	0.4155	0.6017	2.3513	1.5696	2.1856	-0.0983	-0.8764	-0.1303	0.0553	0.262	0.0538	0.1237	-0.0931	-0.1637	0.3728	0.0019	-0.024	0.6832	0.1317	0.1778	22.7817	61.5904	45.4273
5	5.2955	-0.6967	1.7869	0.4489	0.4275	2.114	0.0711	0.0044	-0.4352	-0.0073	0.0328	0.0085	-0.0309	-0.0364	-0.1039	0.4025	-0.0016	0.008	0.2472	0.0642	0.2957	19.919	56.0616	23.8389
6	2.6515	-0.1684	0.0802	1.1809	0.3506	0.3427	0.3741	-0.2854	-1.2525	0.1636	0.0694	-0.2121	0.3364	0.0097	-0.4434	0.4929	-0.0125	-0.3022	0.2112	0.1365	0.9083	26.2259	43.5907	27.1554
7	11.7072	0.4499	4.3804	0.3537	-0.33	2.7507	0.0272	0.2072	-0.1789	-0.0597	0.0304	0.0703	0.0034	0.1972	-0.0576	0.3796	0.0194	0.0009	0.2486	-0.0699	0.3556	29.1832	55.2007	18.071
8	3.0909	-0.7628	1.1266	1.6897	-0.6345	2.2048	0.4503	0.1118	-1.0639	-0.0919	0.0072	0.1527	0.4568	0.1352	-0.4575	0.4143	0.0069	-0.2069	0.0888	-0.0262	0.6521	22.7205	42.6051	20.1021
9	6.4913	-2.7772	0.3339	1.9497	-0.8787	1.0241	0.0464	0.6008	0.1016	0.124	0.0382	0.0541	-0.0384	0.0765	-0.0846	0.3746	0.0283	0.0162	0.4716	-0.0629	0.2511	20.4497	61.1252	6.9719
10	1.2471	0.227	0.7227	0.1233	0.1917	3.9419	0.2287	0.8661	-0.3855	-0.1437	-0.0149	0.004	0.5591	0.4052	-0.2138	0.4	0.2419	-0.125	0.8046	-0.2893	0.264	26.6525	54.7741	-3.9469
11	6.0698	-1.7977	1.5054	2.0721	-0.3787	0.4144	0.098	0.4689	0.196	0.033	-0.1313	-0.1064	-0.0052	-0.0286	0.0333	0.3567	0.0183	0.0326	0.5572	0.061	0.184	29.346	66.5402	4.3947
12	4.0446	-1.2443	-1.4533	3.3676	1.1309	2.6657	0.8729	2.257	-0.2984	-0.885	-0.9465	0.2067	-0.0543	-0.125	0.0736	0.4582	0.5654	-0.1631	1.4628	-0.2208	0.0178	22.9474	61.4933	-7.0871
13	5.0533	-1.5175	-1.2936	1.2471	0.6329	0.9869	0.0021	0.2361	0.9606	-0.0808	0.0869	-0.1533	0.0614	-0.0758	-0.089	0.3236	0.0035	-0.002	0.2633	0.1451	0.5226	29.0869	83.2963	11.0307
14	2.9589	-0.3929	-1.7529	1.9529	0.4522	4.2064	0.3292	0.6494	1.1397	-0.4811	0.0078	-0.1246	-0.4594	-0.319	-0.337	0.3585	0.1262	0.1254	0.3226	0.4453	0.903	23.441	93.0691	2.9963
15	5.8557	-1.6833	-1.4431	1.6575	1.4173	1.2967	-0.1345	0.4927	0.5707	0.0801	-0.0803	0.0879	0.2341	-0.0699	0.2147	0.3312	-0.0042	0.063	0.4075	0.2489	0.4374	20.681	79.0761	6.4709
16	4.7474	-3.343	0.0704	4.2	0.2129	1.0514	0.589	1.7445	1.3496	-0.7614	-0.6202	-0.536	-0.4009	0.0809	0.0312	0.4264	0.2388	0.2084	0.9335	0.6702	0.5895	27.0815	88.007	-2.3034
17	5.4168	0.8366	-1.3419	0.4137	-0.453	1.009	-0.1683	0.1506	0.6505	-0.1281	0.1148	0.0051	0.0344	-0.1328	0.0535	0.301	-0.0101	0.0162	0.2199	-0.0683	0.6332	20.6292	85.0628	23.7002
18	1.4136	-0.308	-0.2422	1.938	2.1135	2.7318	0.1781	-0.2693	1.325	-0.0738	0.1282	-0.3063	-0.187	0.2059	-0.3063	0.3129	0.0015	0.1809	0.2237	-0.2483	1.512	26.8536	96.5124	28.7097
19	5.1836	0.9899	-1.2325	0.5828	-0.6107	0.8203	-0.0847	-0.3429	0.5814	-0.0219	0.0087	0.0083	0.0743	0.0062	0.076	0.3246	0.0172	0.0139	0.2564	-0.1728	0.5567	29.2859	82.1775	28.8558
20	1.8977	1.2658	0.1375	3.455	-0.4986	0.5793	0.0518	-0.3711	0.7843	0.249	0.0024	-0.0275	-0.1933	-0.1063	-0.0542	0.2887	0.021	0.0697	0.3099	-0.3032	0.6573	23.3957	92.8761	35.8523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 45
2	X-RAY DIFFRACTION	2	A	46 - 93
3	X-RAY DIFFRACTION	3	B	4 - 45
4	X-RAY DIFFRACTION	4	B	46 - 93
5	X-RAY DIFFRACTION	5	C	4 - 45
6	X-RAY DIFFRACTION	6	C	46 - 93
7	X-RAY DIFFRACTION	7	D	4 - 45
8	X-RAY DIFFRACTION	8	D	46 - 94
9	X-RAY DIFFRACTION	9	E	4 - 45
10	X-RAY DIFFRACTION	10	E	46 - 93
11	X-RAY DIFFRACTION	11	F	4 - 45
12	X-RAY DIFFRACTION	12	F	46 - 94
13	X-RAY DIFFRACTION	13	G	4 - 45
14	X-RAY DIFFRACTION	14	G	46 - 93
15	X-RAY DIFFRACTION	15	H	4 - 45
16	X-RAY DIFFRACTION	16	H	46 - 94
17	X-RAY DIFFRACTION	17	I	4 - 45
18	X-RAY DIFFRACTION	18	I	46 - 93
19	X-RAY DIFFRACTION	19	J	4 - 45
20	X-RAY DIFFRACTION	20	J	46 - 93

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