PDB-2pd1: Crystal structure of NE2512 protein of unknown function from Nitr...

ID or keywords:

Entry

Database: PDB / ID: 2pd1

Title

Crystal structure of NE2512 protein of unknown function from Nitrosomonas europaea

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NE2512 protein / APC7253 / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta /

ACETATE ION / Uncharacterized protein

Function and homology information

Biological species

Nitrosomonas europaea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.86 Å

Authors

Osipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of NE2512 protein of unknown function from Nitrosomonas europaea.
Authors: Osipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Mar 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Remark 300

BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2pd1.cif.gz	93.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2pd1.ent.gz	78.7 KB	Display	PDB format
PDBx/mmJSON format	2pd1.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/pd/2pd1 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/2pd1	HTTPS FTP

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Related structure data

Similar structure data	6t84-d 1fpz-1 2kku-d 1kk9-d 3w6k-1 4ly5-d 6ydc-3 6gtr-2 4r30-1 4pjy-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search
Other databases	TargetDB: APC7253

Similar structure data

Other databases

TargetDB: APC7253

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

C: Hypothetical protein

D: Hypothetical protein

hetero molecules

43.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypothetical protein

C: Hypothetical protein

hetero molecules

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

2

B: Hypothetical protein

D: Hypothetical protein

hetero molecules

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

3

A: Hypothetical protein

C: Hypothetical protein

hetero molecules

A: Hypothetical protein

C: Hypothetical protein

hetero molecules

B: Hypothetical protein

D: Hypothetical protein

hetero molecules

B: Hypothetical protein

D: Hypothetical protein

hetero molecules

defined by software
86.6 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

Idetical with deposited unit
defined by software

5

A: Hypothetical protein

C: Hypothetical protein

hetero molecules

B: Hypothetical protein

D: Hypothetical protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.308, 68.137, 162.645
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-604- HOH
2	1	C-605- HOH

#1: Protein	Hypothetical protein / Mass: 10781.974 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: IFO 14298 / Gene: NE2512 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82S47
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.16 Å³/Da / Density % sol: 43.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Na Acetate, 0.15M Bis-Tris pH 6.5, 36% PEG8000, 2% Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.86→35.9 Å / Num. all: 31503 / Num. obs: 31503 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / B_iso Wilson estimate: 30.2 Å² / R_merge(I) obs: 0.109 / Net I/σ(I): 24.4
Reflection shell	Resolution: 1.86→1.91 Å / Redundancy: 5 % / R_merge(I) obs: 0.617 / Mean I/σ(I) obs: 2.11 / Num. unique all: 2124 / % possible all: 86.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.86→35.9 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / SU B: 5.245 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1854	1590	5.1 %	RANDOM
R_work	0.1584	-	-	-
all	0.1598	29824	-	-
obs	0.1598	29824	98.36 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.166 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1 Å²	0 Å²	0 Å²
2-	-	-0.81 Å²	0 Å²
3-	-	-	-0.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→35.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2942	0	12	404	3358

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	3071
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.553	1.979	4187
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.559	5	421
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.446	25.351	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.913	15	471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.118	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	488
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2334
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1400
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	2132
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	368
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	0.224	0.2	65
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.211	0.2	31
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	0.947	1.5	2102
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.4	2	3226
X-RAY DIFFRACTION	r_scbond_it	2.529	3	1076
X-RAY DIFFRACTION	r_scangle_it	3.763	4.5	951
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.86→1.906 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	105	-
R_work	0.223	1884	-
obs	-	1989	85.15 %

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	3.8456	-0.711	-1.0889	7.8409	2.3634	0.9147	-0.1185	0.5612	-0.3523	-0.6692	-0.152	0.0054	-0.3352	-0.0615	0.2705	0.1375	0.0077	0.0329	0.0936	-0.0708	0.0488	5.4396	5.9858	5.4908
2	1.4796	0.0079	-0.1933	0.4134	-0.1422	1.9665	-0.0089	0.0169	0.0645	0.078	-0.0146	-0.0961	-0.0697	0.0125	0.0236	0.0541	-0.0059	-0.0073	0.0484	-0.0082	0.0605	11.8273	22.4987	20.9475
3	0.8823	-0.3334	-0.212	0.2321	0.018	0.0873	0.0063	0.0336	-0.0166	0.0224	-0.0401	-0.056	-0.0111	-0.0024	0.0337	0.0604	-0.01	0.0116	0.0743	-0.0141	0.0508	9.0656	17.342	10.5282
4	1.4231	0.9055	0.7311	1.8052	1.248	0.8742	0.1033	-0.0461	-0.2004	0.1152	-0.1024	-0.1318	0.0827	-0.0482	-0.0009	0.0921	0.0101	-0.0004	0.0562	0.0087	0.0562	16.7897	9.1437	8.6223
5	1.6931	-1.5677	-1.4994	4.7108	1.6383	1.3469	0.1444	-0.1798	0.1529	-0.2645	-0.0024	-0.0657	0.2976	0.0793	-0.142	0.0879	0.0039	-0.0297	0.0623	0.0189	0.0461	17.9344	17.2965	23.4497
6	1.5228	1.6626	2.395	4.061	4.4216	7.2007	0.1673	0.0831	-0.3623	0.28	0.1066	-0.298	0.2253	0.0776	-0.2739	0.0367	0.0096	-0.0069	0.037	-0.0069	0.0959	6.8076	4.5206	13.9347
7	0.6707	-1.7873	2.2663	26.0354	-12.5953	9.6786	-0.4364	-0.0435	-0.5694	-0.5962	0.0018	-0.5999	0.1069	0.4549	0.4346	0.1062	-0.0062	0.018	0.0856	0.0011	-0.021	-0.1554	10.1734	-0.4765
8	7.4846	-2.9332	-2.2516	11.6043	-1.337	1.1485	-0.0053	-0.9221	0.3116	0.6598	-0.2804	-0.5724	0.5192	-0.2459	0.2857	0.057	0	-0.0048	0.1271	0.0211	0.0938	-7.216	23.8982	33.0307
9	1.9875	0.8642	0.7473	1.419	1.5588	1.7403	-0.1073	0.1045	0.0844	-0.1549	-0.0068	0.131	-0.1295	0.0293	0.1141	0.0746	-0.0007	-0.0424	0.0548	0.0217	0.0769	-25.2661	19.0832	18.5575
10	0.039	-0.0891	-0.1026	0.9625	-0.132	0.4474	-0.0526	-0.0085	0.0277	0.0612	-0.0006	0.1017	0.0364	-0.0426	0.0532	0.0536	-0.0067	-0.0051	0.0588	0.008	0.0694	-20.9224	19.6339	30.3657
11	2.9851	-1.6643	0.6163	1.0658	-1.0756	4.2483	-0.0393	-0.1928	0.2953	0.0052	-0.0734	-0.1304	0.2463	0.0246	0.1127	0.0562	0.0007	-0.0105	0.047	0.0108	0.0859	-6.5486	18.6783	34.4686
12	1.8548	0.5982	0.7226	0.332	0.6623	1.6057	0.0529	0.1304	-0.055	-0.0175	0.0003	-0.0705	-0.056	-0.0222	-0.0532	0.0805	0.0079	0.0214	0.0506	0.028	0.0634	-14.9759	10.7299	26.907
13	5.0663	3.6932	4.6111	3.5777	3.5695	4.5603	-0.0895	0.1664	-0.1913	-0.338	0.2045	-0.2815	-0.1344	0.1514	-0.115	0.0786	0.0007	0.0324	0.0302	-0.0109	0.0528	-14.1504	18.7563	20.142
14	18.2656	-4.2017	-10.491	1.3635	3.4774	8.8777	-0.467	-0.892	-0.4651	0.2598	0.0662	0.1075	0.3693	0.5053	0.4008	0.1054	0.001	-0.0063	0.0558	0.0215	0.0577	-9.7771	30.3945	38.9111
15	2.9319	-1.3072	1.5334	3.636	1.4493	2.2922	-0.1016	0.2748	0.2073	-0.2929	-0.0072	-0.101	-0.0184	0.0875	0.1088	0.0568	-0.001	0.0111	0.056	-0.0054	0.1125	-1.793	17.5812	11.6016
16	1.5828	0.4229	0.408	1.5285	-0.6124	1.1379	-0.0022	-0.0185	-0.0044	-0.0372	0.0059	0.0183	0.1294	-0.0251	-0.0037	0.0629	-0.0025	0.0062	0.0363	-0.0066	0.0678	-9.929	-1.8029	13.5899
17	0.7625	0.1042	0.4251	0.0179	0.0687	0.2677	0.0118	0.0627	-0.0119	-0.0268	-0.0044	-0.0106	0.026	0.0365	-0.0074	0.0761	-0.0009	-0.0046	0.0538	-0.0044	0.0598	-4.8304	9.342	6.571
18	3.8372	2.0937	0.4588	5.1573	-0.4946	0.1931	0.0034	0.0292	0.169	0.0814	-0.0234	0.1154	0.0193	-0.119	0.02	0.057	0.0178	-0.0024	0.0774	-0.0033	0.0411	-12.6998	17.4753	8.2477
19	4.5079	0.7637	4.0802	4.6766	2.3278	5.0118	0.0629	-0.0788	0.0866	0.0464	0.0327	0.1087	-0.0807	-0.1907	-0.0956	0.0653	-0.0091	0.0421	0.047	0.0035	0.0452	-14.7829	3.7538	17.8336
20	9.3925	12.0595	-5.1497	17.5504	-6.3299	3.4515	0.1281	-0.0694	0.2057	0.2628	-0.0889	0.1421	-0.0149	-0.18	-0.0392	0.0906	-0.0067	-0.0011	0.056	-0.0117	0.0311	-3.1138	19.3351	16.3854
21	2.9463	-3.2984	-7.7391	12.6417	10.4989	20.7047	-0.0631	-0.0234	0.1824	-0.6784	-0.0794	-0.0323	-0.2505	-1.1036	0.1425	0.0768	-0.0026	0.0016	0.1258	-0.0182	0.0346	6.2705	19.7905	2.4812
22	8.5729	-4.5967	0.5777	8.3485	5.1105	5.0321	0.0673	-1.0365	-0.1147	0.4047	-0.0709	0.852	0.3758	0.1322	0.0037	0.0359	0.0066	0.01	0.1027	0.0165	0.0962	-23.512	30.7296	32.7454
23	1.5506	2.2439	0.4635	3.3786	0.2554	1.4522	-0.1725	0.0552	0.0589	-0.1628	0.1512	-0.0643	0.0542	0.0624	0.0214	0.0419	0.0047	0.0152	0.0418	0.0133	0.0761	-3.0781	38.2657	21.8479
24	0.1275	0.1372	-0.1541	1.236	-0.2395	0.1914	-0.0513	-0.0191	-0.014	0.0609	0.0207	-0.1133	0.0356	0.0114	0.0305	0.0475	0.0034	0.0094	0.0697	-0.0151	0.069	-9.9459	35.4901	33.0364
25	0.3584	1.4199	0.1714	7.0394	0.4606	0.1156	-0.164	-0.0034	0.1727	-0.0511	0.1329	0.3064	-0.0669	-0.0628	0.0311	0.0683	0.0121	0.0128	0.0576	-0.0162	0.0701	-23.4468	40.7689	33.2328
26	0.1519	-0.3463	-0.1303	1.7427	-0.6409	1.0349	0.0178	-0.0088	0.0338	-0.0081	0.0374	-0.0486	-0.0722	0.0305	-0.0552	0.0405	0.0011	0.0156	0.0706	-0.0093	0.0682	-8.9594	45.6024	25.3688
27	7.0426	7.2542	-3.7757	8.9153	-6.2667	5.9411	-0.1894	0.1482	-0.0363	-0.2844	0.2123	0.0368	0.1417	-0.0425	-0.0229	0.0524	0.0097	-0.018	0.0349	0.0083	0.0997	-20.5287	34.644	23.6709
28	13.1312	-3.9855	9.6334	10.308	-9.4238	11.7109	-0.3573	-1.0995	0.3682	0.81	-0.205	-0.384	-0.8636	-0.6816	0.5624	0.12	0.029	-0.0029	0.146	-0.0546	0.0708	-20.7775	24.0966	38.3843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-1 - 8	1 - 10
2	X-RAY DIFFRACTION	2	A	A	9 - 27	11 - 29
3	X-RAY DIFFRACTION	3	A	A	28 - 55	30 - 57
4	X-RAY DIFFRACTION	4	A	A	56 - 74	58 - 76
5	X-RAY DIFFRACTION	5	A	A	75 - 86	77 - 88
6	X-RAY DIFFRACTION	6	A	A	87 - 93	89 - 95
7	X-RAY DIFFRACTION	7	A	A	94 - 101	96 - 103
8	X-RAY DIFFRACTION	8	B	B	1 - 7	3 - 9
9	X-RAY DIFFRACTION	9	B	B	8 - 21	10 - 23
10	X-RAY DIFFRACTION	10	B	B	22 - 53	24 - 55
11	X-RAY DIFFRACTION	11	B	B	54 - 60	56 - 62
12	X-RAY DIFFRACTION	12	B	B	61 - 79	63 - 81
13	X-RAY DIFFRACTION	13	B	B	80 - 92	82 - 94
14	X-RAY DIFFRACTION	14	B	B	93 - 100	95 - 102
15	X-RAY DIFFRACTION	15	C	C	1 - 9	3 - 11
16	X-RAY DIFFRACTION	16	C	C	10 - 24	12 - 26
17	X-RAY DIFFRACTION	17	C	C	25 - 57	27 - 59
18	X-RAY DIFFRACTION	18	C	C	58 - 74	60 - 76
19	X-RAY DIFFRACTION	19	C	C	75 - 86	77 - 88
20	X-RAY DIFFRACTION	20	C	C	87 - 93	89 - 95
21	X-RAY DIFFRACTION	21	C	C	94 - 101	96 - 103
22	X-RAY DIFFRACTION	22	D	D	1 - 7	3 - 9
23	X-RAY DIFFRACTION	23	D	D	8 - 21	10 - 23
24	X-RAY DIFFRACTION	24	D	D	22 - 57	24 - 59
25	X-RAY DIFFRACTION	25	D	D	58 - 67	60 - 69
26	X-RAY DIFFRACTION	26	D	D	68 - 85	70 - 87
27	X-RAY DIFFRACTION	27	D	D	86 - 92	88 - 94
28	X-RAY DIFFRACTION	28	D	D	93 - 101	95 - 103

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