PDB-2gfq: Structure of Protein of Unknown Function PH0006 from Pyrococcus h...

ID or keywords:

Entry

Database: PDB / ID: 2gfq

Title

Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii

Components

UPF0204 protein PH0006

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii / ph0006 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

D-aminoacyl-tRNA deacylase activity / D-aminoacyl-tRNA deacylase / D-amino acid catabolic process / zinc ion binding
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Cuff, M.E. / Skarina, T. / Gorodichtchenskaia, E. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of hypothetical protein ph0006 from Pyrococcus horikoshii
Authors: Cuff, M.E. / Skarina, T. / Gorodichtchenskaia, E. / Edwards, A. / Savchenko, A. / Joachimiak, A.

History

Deposition	Mar 22, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...

Remark 999

SEQUENCE Authors indicate that the conflict with the database involving residue 34 which is an Asp ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gfq.cif.gz	206.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2gfq.ent.gz	174.1 KB	Display	PDB format
PDBx/mmJSON format	2gfq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2gfq_validation.pdf.gz	467.8 KB	Display	wwPDB validaton report
Full document	2gfq_full_validation.pdf.gz	473.3 KB	Display
Data in XML	2gfq_validation.xml.gz	42.1 KB	Display
Data in CIF	2gfq_validation.cif.gz	64.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gf/2gfq ftp://data.pdbj.org/pub/pdb/validation_reports/gf/2gfq	HTTPS FTP

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Related structure data

Similar structure data	5hyx-d 5hz1-d 5le2-2 3l7m-2 3nb2-4 5hz0-d 5hz3-d 3l7k-2 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	TargetDB: apc5769

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UPF0204 protein PH0006

B: UPF0204 protein PH0006

C: UPF0204 protein PH0006

hetero molecules

104 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	65.021, 67.029, 111.572
Angle α, β, γ (deg.)	90.00, 90.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	UPF0204 protein PH0006 Mass: 34080.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0006 / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57774
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1036 / 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: 2.46 Å³/Da / Density % sol: 50.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.3M ammonium sulfate, 2% PEG MME 2K, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2005
Radiation	Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.75→35.8 Å / Num. all: 91292 / Num. obs: 91292 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / B_iso Wilson estimate: 29.3 Å² / R_merge(I) obs: 0.047 / R_sym value: 0.047 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.194 / Mean I/σ(I) obs: 4.2 / % possible all: 94.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data scaling
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
Coot		model building
O		model building
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.75→35.8 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.958 / SU B: 3.284 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17904	4552	5 %	RANDOM
R_work	0.15049	-	-	-
all	0.15193	86739	-	-
obs	0.15193	86739	94.3 %	-

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: 18.001 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.84 Å²	0 Å²	0.46 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	-1.52 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→35.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6719	0	88	1036	7843

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	7027
X-RAY DIFFRACTION	r_angle_refined_deg	1.302	1.968	9488
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.456	5	859
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.375	24.475	324
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.956	15	1260
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.288	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	999
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5262
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	3579
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	4780
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	850
X-RAY DIFFRACTION	r_metal_ion_refined	0.067	0.2	3
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.208	0.2	97
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.176	0.2	83
X-RAY DIFFRACTION	r_mcbond_it	0.896	1.5	4377
X-RAY DIFFRACTION	r_mcangle_it	1.124	2	6795
X-RAY DIFFRACTION	r_scbond_it	2.499	3	3043
X-RAY DIFFRACTION	r_scangle_it	3.414	4.5	2693

LS refinement shell

Resolution: 1.75→1.796 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.233	293	-
R_work	0.178	6094	-
obs	-	-	89.69 %

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	5.9406	-2.6652	3.2691	3.4503	-2.532	11.5104	0.0802	-0.1177	-0.1969	0.1109	0.1829	0.0236	0.0529	-0.0391	-0.263	-0.0046	0.0227	-0.0303	-0.0096	0.0063	0.0531	5.1983	-10.8086	75.0589
2	0.1719	0.0202	0.0339	0.8237	-0.0098	0.8056	0.0095	-0.0492	-0.0352	0.0623	0.0325	0.0588	-0.0121	-0.0543	-0.042	0.0211	0.0048	-0.0041	-0.0055	0.0042	0.0116	-2.3546	3.6253	68.0255
3	0.2694	-0.3239	0.146	1.3394	-0.9521	1.113	-0.0241	-0.0548	0.0109	0.1552	0.0211	0.0405	-0.1077	0.023	0.0029	0.0269	0.0063	-0.0181	-0.0054	-0.0076	0.0097	2.5239	11.1023	68.7826
4	3.0652	1.3091	-0.0095	1.7896	0.2077	3.4904	0.1028	-0.2026	0.3776	0.2613	-0.1263	0.1449	-0.1846	0.0113	0.0235	0.0726	-0.0036	-0.0098	-0.0254	-0.0393	0.0444	8.48	23.2625	74.852
5	0.3143	0.0671	-0.0189	0.5177	-0.0893	0.6376	-0.0268	0.0005	0.006	-0.0074	0.0241	0.0316	-0.0208	0.0127	0.0026	0.0249	0.0035	-0.0136	-0.0255	-0.0041	0.0075	3.4813	13.9155	59.1189
6	15.3368	15.7767	-6.6358	24.6257	-1.4304	6.3385	-0.2876	-0.1933	0.4041	-1.4969	0.5015	-0.6472	0.49	0.1556	-0.2139	0.0101	0.1397	0.0239	0.0317	0.0063	0.1544	19.4696	5.3351	55.8784
7	1.0368	0.265	0.2852	0.7727	0.3435	0.6281	0.0014	-0.0149	0.0728	0.0066	-0.0137	-0.1072	-0.0429	0.0697	0.0123	0.0292	-0.0113	-0.0165	-0.008	-0.0034	0.0265	15.7841	24.8554	61.7424
8	1.2815	-1.2499	-1.8442	5.8368	2.3148	3.9354	-0.0369	-0.1523	-0.0361	0.1299	0.0673	-0.4016	-0.0189	0.1242	-0.0304	0.0049	-0.0088	-0.046	0.0145	-0.0056	0.0519	20.265	16.2016	69.8761
9	2.5224	-1.1821	0.2529	2.6104	0.4907	0.4351	-0.0736	-0.0535	0.112	-0.058	0.1346	-0.1777	-0.0406	0.1123	-0.061	0.0271	-0.0266	-0.0083	0.0151	-0.0221	0.0602	24.0078	29.7238	62.6818
10	0.8454	-0.3682	0.6505	1.1165	-0.3054	1.2251	0.0304	0.1975	0.064	-0.0946	-0.0255	-0.0075	0.0075	0.0448	-0.0049	0.0144	-0.0006	-0.0091	0.0391	-0.0084	0.0009	21.2458	55.3393	70.9934
11	1.4228	0.7301	0.7585	9.7417	2.846	3.1404	0.0882	0.2457	0.0276	-0.5975	-0.0419	-0.0554	-0.1913	-0.0179	-0.0463	-0.0253	0.0134	-0.0051	0.0851	0.0224	0.0071	20.1566	57.3302	63.7966
12	0.9383	0.0793	0.1051	2.0499	-0.2554	1.2967	0.0753	0.1949	-0.0656	-0.1708	-0.0318	-0.0196	0.1127	0.0175	-0.0435	0.0046	0.0046	-0.0202	0.0625	-0.024	0.0129	24.2868	47.7252	67.4085
13	1.579	-0.1511	0.174	0.5408	0.3949	0.341	0.0142	-0.0313	-0.1216	0.063	0.0069	0.027	0.0534	-0.0568	-0.0211	0.0013	-0.0047	-0.0015	0.007	0.0071	0.0041	24.9877	46.2481	85.0356
14	1.0536	-0.3255	0.117	0.9483	0.08	0.9431	0.0039	0.0392	-0.0321	0.0218	0.0061	-0.0422	-0.025	0.0333	-0.01	-0.0201	-0.0087	-0.0084	0.0015	0.0023	0.0075	29.7301	50.5126	83.689
15	2.464	0.1942	-0.2644	1.5264	-0.5947	1.131	0.0031	0.1138	0.1794	0.0034	-0.0299	-0.0357	-0.155	0.0118	0.0268	0.0104	-0.0121	-0.0263	0	-0.0064	-0.0144	25.9637	60.0283	81.22
16	1.3232	-0.3898	0.3221	0.7963	-0.1928	0.9308	-0.0096	-0.0804	0.0103	0.0799	-0.015	-0.0689	0.0132	0.1484	0.0246	-0.0138	-0.0018	-0.0128	0.0305	0.0111	0.02	38.092	47.0657	91.9725
17	1.19	-0.4664	0.6321	0.9752	-0.4664	2.6157	-0.0092	0.0523	-0.0298	0.0384	-0.0673	-0.1237	-0.0129	0.2638	0.0765	-0.0314	-0.0014	-0.0041	0.0307	0.022	0.062	42.8374	45.0754	89.1778
18	2.5835	0.4174	-1.8331	2.7898	-1.8453	3.3749	-0.0898	-0.0541	-0.0647	0.0753	-0.0984	-0.2607	0.0743	0.2391	0.1882	-0.0093	0.0118	-0.0342	0.0821	0.0373	0.0467	47.3816	41.7156	95.8589
19	0.7704	-0.4592	-1.4483	1.3676	0.6343	3.1501	-0.0207	0.0024	-0.0665	-0.0256	0.0245	-0.0549	-0.0313	0.1991	-0.0039	-0.0099	-0.008	-0.0038	0.0054	0.0015	-0.0108	24.4712	54.039	109.4175
20	2.0453	2.1427	-1.031	16.9264	6.6707	8.6872	0.0978	0.0213	0.1365	-0.793	0.1101	-0.2369	-0.9018	0.2181	-0.2078	0.051	-0.0362	0.0078	0.0055	0.0201	-0.0208	26.7724	63.35	101.8307
21	1.0074	0.332	-0.836	1.4188	0.5904	2.825	0.1019	-0.0633	0.1021	0.0173	0.0039	0.0319	-0.2937	0.1159	-0.1058	0.0016	-0.0191	-0.0014	0.013	-0.0129	-0.0047	20.1646	62.4512	113.3476
22	1.4429	0.1982	-1.4254	0.8798	0.1077	2.2962	-0.1706	-0.1761	-0.135	0.0734	-0.0207	-0.0195	0.32	0.1737	0.1913	0.0456	0.0112	0.0298	0.0148	0.0116	-0.0184	16.1306	47.6604	121.9488
23	3.8834	-1.3278	0.6824	1.2525	-0.8671	3.5302	-0.2966	0.0563	-0.2632	0.0722	0.0086	-0.0349	0.4308	0.2237	0.288	0.0799	0.0248	0.0637	-0.0109	0.0252	0.0259	22.9478	43.9882	111.9481
24	120.8935	71.9059	-22.6208	43.7574	-21.8506	75.5309	0.0538	2.0296	1.7495	0.9361	0.8148	0.8792	3.1632	-3.0402	-0.8686	0.1169	0.0103	-0.1313	0.1899	-0.0657	0.1714	2.7204	47.9721	106.176
25	1.4005	0.081	-1.12	0.9317	-0.7595	2.8218	-0.1927	0.0096	-0.2071	-0.1643	0.0255	-0.0458	0.4399	-0.052	0.1672	0.089	-0.0339	0.0565	0.0184	-0.0181	0.0061	6.5139	41.6297	125.6283
26	2.4621	0.5836	-1.5389	1.74	-0.653	8.0758	0.0523	0.1137	0.0225	0.0951	0.1268	0.2083	-0.1871	-0.6018	-0.1792	-0.0185	0.0107	0.0289	0.0526	0.0094	0.0224	-0.0328	54.0447	127.1329
27	2.3541	0.0279	-0.8015	1.2875	-0.9132	5.6094	-0.2658	0.1531	-0.0874	-0.0196	0.1671	0.0522	0.3915	-0.4756	0.0987	0.0488	-0.075	0.0234	0.0833	0.0019	-0.0018	-2.8701	41.845	131.4686

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	-12 - -2	10 - 20
2	X-RAY DIFFRACTION	2	A	A	-1 - 60	21 - 82
3	X-RAY DIFFRACTION	3	A	A	61 - 91	83 - 113
4	X-RAY DIFFRACTION	4	A	A	92 - 109	114 - 131
5	X-RAY DIFFRACTION	5	A	A	110 - 182	132 - 204
6	X-RAY DIFFRACTION	6	A	A	183 - 188	205 - 210
7	X-RAY DIFFRACTION	7	A	A	189 - 232	211 - 254
8	X-RAY DIFFRACTION	8	A	A	233 - 241	255 - 263
9	X-RAY DIFFRACTION	9	A	A	242 - 275	264 - 297
10	X-RAY DIFFRACTION	10	B	B	-4 - 22	18 - 44
11	X-RAY DIFFRACTION	11	B	B	23 - 34	45 - 56
12	X-RAY DIFFRACTION	12	B	B	35 - 70	57 - 92
13	X-RAY DIFFRACTION	13	B	B	71 - 102	93 - 124
14	X-RAY DIFFRACTION	14	B	B	103 - 156	125 - 178
15	X-RAY DIFFRACTION	15	B	B	157 - 188	179 - 210
16	X-RAY DIFFRACTION	16	B	B	189 - 232	211 - 254
17	X-RAY DIFFRACTION	17	B	B	233 - 252	255 - 274
18	X-RAY DIFFRACTION	18	B	B	253 - 275	275 - 297
19	X-RAY DIFFRACTION	19	C	C	-3 - 24	19 - 46
20	X-RAY DIFFRACTION	20	C	C	25 - 32	47 - 54
21	X-RAY DIFFRACTION	21	C	C	33 - 75	55 - 97
22	X-RAY DIFFRACTION	22	C	C	76 - 155	98 - 177
23	X-RAY DIFFRACTION	23	C	C	156 - 182	178 - 204
24	X-RAY DIFFRACTION	24	C	C	183 - 187	205 - 209
25	X-RAY DIFFRACTION	25	C	C	189 - 227	211 - 249
26	X-RAY DIFFRACTION	26	C	C	228 - 242	250 - 264
27	X-RAY DIFFRACTION	27	C	C	243 - 275	265 - 297

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