PDB-2hqy: Crystal Structure of Conserved Protein of Unknown Function from B...

ID or keywords:

Entry

Database: PDB / ID: 2hqy

Title

Crystal Structure of Conserved Protein of Unknown Function from Bacteroides thetaiotaomicron VPI-5482

Components

conserved hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / MCSG / PSI2 / MAD /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

membrane => GO:0016020 /

plasma membrane
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Nocek, B. / Borovilos, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of conserved hypothetical protein from Bacteroides thetaiotaomicron VPI-5482
Authors: Nocek, B. / Borovilos, M. / Abdullah, J. / Joachimiak, A.

History

Deposition	Jul 19, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 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 2 CHAINS. ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2hqy.cif.gz	147.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2hqy.ent.gz	124.8 KB	Display	PDB format
PDBx/mmJSON format	2hqy.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/hq/2hqy ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqy	HTTPS FTP

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Related structure data

Similar structure data	1xcq-4 3ilv-d 6aek-d 4gtw-2 5c1d-d 0274 5npr-d 6axf-2 4gty-2 1xcq-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: APC82027

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #93 - Sep 2007 Citrate Synthase similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: conserved hypothetical protein

B: conserved hypothetical protein

hetero molecules

71.7 kDa, 2 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)	66.468, 81.879, 138.449
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MET / Refine code: 4

Dom-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	HIS	A	A	1 - 298	1 - 298
2	LYS	B	B	1 - 296	1 - 296

#1: Protein	conserved hypothetical protein Mass: 35483.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_3689 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A1H2
#2: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.65 Å³/Da / Density % sol: 53.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 3M Magnesium Formate 0.1 M BisTris, pH 5.4 10mM CoA, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97936, 0.97953

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2006

Radiation

Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97936	1
2	0.97953	1

Reflection

Resolution: 1.8→40 Å / Num. all: 71360 / Num. obs: 70650 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.078 / Net I/σ(I): 17.1

Reflection shell

Resolution: 1.8→1.847 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.649 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.8→40 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.944 / SU B: 4.243 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21125	3569	5.1 %	RANDOM
R_work	0.17559	-	-	-
all	0.1774	70650	-	-
obs	0.1774	67054	99.82 %	-

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: 22.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.55 Å²	0 Å²	0 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4836	0	48	613	5497

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	5041
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.427	1.958	6855
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.825	5	628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.623	24.229	253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.376	15	866
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.988	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	744
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3878
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	2408
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	3540
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	507
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	0.222	0.2	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.208	0.2	30
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	0.889	1.5	3114
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.455	2	4888
X-RAY DIFFRACTION	r_scbond_it	2.347	3	2207
X-RAY DIFFRACTION	r_scangle_it	3.375	4.5	1954
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2270 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.57	0.5
medium thermal	1.83	2

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.287	252	-
R_work	0.238	4904	-
obs	-	-	99.71 %

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	1.4587	-0.6563	1.1108	1.7836	-0.0911	3.2062	-0.2229	0.1283	0.3315	-0.0249	0.0399	-0.0546	-0.3426	0.4033	0.183	0.064	-0.0459	-0.0342	0.0019	0.0303	0.0623	46.3317	55.5646	6.571
2	0.7073	-0.4538	-0.2573	0.6335	0.8752	1.5666	-0.0889	0.1058	-0.0018	-0.0329	-0.0264	0.0008	-0.1475	-0.0842	0.1153	0.0465	0.011	-0.0191	0.0361	0.0235	0.0551	39.0261	48.7516	10.8844
3	1.5421	-0.9314	0.7703	1.0039	0.0667	1.8948	0.0685	0.1948	0.015	-0.0603	-0.1931	-0.0191	-0.1908	-0.0374	0.1246	0.0634	0.0393	-0.0359	0.0408	0.0202	0.0275	37.229	52.4724	-3.402
4	8.6282	4.307	1.6034	10.7997	-4.5051	3.6295	-0.0038	-0.4615	1.3456	1.3045	-0.3355	1.6633	-0.9272	-1.0736	0.3392	0.1929	0.0723	0.1032	0.1057	-0.0973	0.2825	23.0661	56.2528	1.4877
5	4.2928	0.97	0.7178	24.8304	-19.7224	22.1383	0.4205	0.2022	0.4796	-0.1003	0.4223	1.3507	-0.1192	-0.9726	-0.8428	-0.0454	0.0691	-0.0747	0.1838	0.049	0.1083	22.1004	50.0662	-4.5851
6	1.2251	1.4003	2.1667	1.6321	2.1667	6.8837	0.0784	-0.0883	-0.028	-0.1035	0.0658	-0.0117	-0.1911	-0.3658	-0.1442	-0.0326	0.0339	-0.013	0.106	-0.0402	0.0495	26.4059	44.9248	18.6839
7	2.8846	0.5139	-0.4597	4.5095	-0.1192	4.7789	-0.0041	-0.1352	0.0348	-0.0735	-0.159	0.3518	-0.0235	-0.8193	0.1631	-0.0405	-0.0134	0.0239	0.2542	-0.0805	0.0257	22.4899	43.0977	34.7685
8	2.0406	0.592	0.9362	0.6514	0.7163	4.4379	0.2264	-0.4902	0.1448	0.1535	-0.2486	0.0072	0.3846	-0.3814	0.0222	0.0713	-0.0503	0.0116	0.1177	-0.0104	-0.0446	36.4794	36.9268	39.5474
9	2.3498	3.1374	1.5143	4.546	2.1584	1.7252	0.0014	-0.1437	-0.0197	0.0479	-0.0243	-0.1044	0.1085	0.0119	0.0229	0.0371	-0.0002	0.0099	0.0343	-0.0121	0.0017	48.2751	33.5943	25.5352
10	0.5457	1.3493	0.1915	3.3513	0.5227	0.2306	-0.0104	0.0111	0.1078	-0.032	0.0449	0.0153	0.0662	0.0314	-0.0345	0.0477	-0.0153	0.0022	0.0308	0.003	0.0195	43.6304	31.8066	13.6129
11	0.3143	0.5481	-0.8708	1.3407	-0.8471	3.5829	-0.0096	-0.1282	0.0584	0.1273	-0.0463	-0.047	-0.0149	0.2337	0.0559	0.0197	0.0071	-0.0051	0.0565	0.0011	0.0144	46.9533	41.0131	27.5277
12	0.0357	-0.1563	0.1488	1.0276	-0.1246	1.4295	-0.0156	-0.0544	0.0288	-0.0404	-0.0578	0.0509	-0.0257	-0.1402	0.0735	0.0247	0.0169	-0.014	0.046	-0.0105	0.0547	37.9316	45.9176	22.5217
13	0.6061	0.433	0.9213	1.8026	-0.6093	2.4765	0.0678	-0.1417	-0.0054	0.013	-0.2262	-0.0037	-0.0135	-0.2974	0.1584	0.0188	-0.0097	0.0181	0.0751	-0.0335	0.0113	35.4921	41.7986	31.8039
14	2.0304	0.253	0.4616	0.6281	0.3697	1.1072	0.0288	-0.0466	-0.0376	-0.0436	-0.055	0.0442	-0.0018	-0.3138	0.0262	-0.0129	0.0135	-0.0251	0.1221	-0.0355	0.0294	26.5728	42.3612	19.2566
15	10.7512	5.3987	-10.3736	6.9968	-6.3099	29.65	0.0186	0.7086	0.1648	-0.5104	0.2284	0.3783	-0.0336	-1.2418	-0.247	0.0088	0.0816	-0.0831	0.1245	0.0131	0.0144	26.0809	48.2695	-6.0879
16	9.6433	-0.3622	10.5135	4.1069	-1.2231	11.6298	-0.7258	-0.3222	0.4304	0.1468	0.0814	-0.2168	-0.7934	-0.534	0.6444	0.0528	0.0516	-0.0161	0.0144	-0.0261	0.0293	59.9341	48.3157	12.8389
17	0.6683	-0.2781	-0.9425	0.7458	0.2818	1.3484	0.0204	0.0454	0.0149	0.0171	0.0249	-0.0083	-0.0365	-0.0019	-0.0454	0.0272	-0.0057	-0.005	0.0259	-0.0055	0.0463	65.7463	44.933	-1.4492
18	1.0179	0.3965	0.221	1.0304	0.4186	0.9225	0.0307	-0.0582	-0.0012	-0.0577	0.0051	0.0146	-0.0018	0.0103	-0.0358	0.0305	0.0016	0.0004	0.0315	-0.0043	0.0382	58.3797	41.7844	6.5464
19	2.7162	0.6204	0.4698	1.1457	-0.4549	1.1389	-0.0219	-0.038	0.0733	0.0124	0.0136	-0.0121	0.0405	0.0717	0.0083	0.0101	0.0073	-0.0083	0.0401	-0.0073	0.0276	67.6107	40.9962	11.2732
20	1.735	-0.716	-1.2452	0.8551	-0.4271	2.4757	-0.0566	-0.1802	0.0321	0.0734	-0.0145	-0.0785	-0.0256	0.0698	0.0711	0.0098	0.0112	-0.0367	0.0754	-0.0116	0.0045	67.4908	38.9208	18.4688
21	7.3267	-2.4553	6.068	6.6945	2.6211	21.6188	-0.1846	0.422	0.1333	-0.3999	0.0831	-1.0369	-0.6005	0.4309	0.1015	-0.1263	-0.043	0.0107	-0.0196	-0.025	0.0528	79.8604	34.8254	9.7788
22	9.5686	4.809	8.4646	6.6813	5.4177	10.3884	0.0695	-0.3443	-0.2288	-0.1744	0.0542	-0.4121	0.4155	0.2472	-0.1238	-0.0337	0.0357	-0.0218	0.0612	0.0051	0.0048	76.4581	28.7358	14.7317
23	0.178	-0.2772	0.323	0.7048	0.1044	1.9368	0.1014	-0.0262	-0.0067	-0.0501	-0.0593	-0.0151	0.0276	0.0427	-0.0421	0.0623	0.0289	0.0048	0.0165	0.0092	0.0194	71.228	26.9484	-16.3052
24	1.3968	-1.5316	0.5797	3.2228	0.3463	2.6903	0.2156	0.1113	0.0239	-0.426	-0.1514	0.1524	0.1141	-0.0321	-0.0642	0.0913	0.0126	-0.0426	0.0438	0.0083	-0.05	57.223	30.3179	-28.6649
25	5.0432	2.894	-0.2911	21.9037	-1.6757	3.8919	0.0365	-0.2578	0.0329	-0.6224	-0.1316	0.3072	0.4137	-1.0288	0.0951	0.0251	-0.0807	-0.0458	0.2176	-0.0217	-0.0164	45.6087	31.849	-14.2584
26	2.2842	0.5855	-0.2201	3.2233	-1.6388	4.9762	0.0864	0.2723	-0.1702	-0.1932	-0.0022	0.1136	0.6473	-0.1963	-0.0842	0.0861	-0.0214	-0.0277	0.0587	-0.023	0.0382	49.6415	30.8458	-3.0862
27	0.3467	-0.5357	-0.7743	1.4943	1.1503	1.7325	0.0387	0.0926	0.0943	-0.2297	-0.0514	0.0896	-0.2634	-0.3994	0.0128	0.0369	0.0056	-0.0207	0.1213	0.0113	0.0018	52.177	39.0723	-16.9918
28	0.4408	0.2577	0.444	0.2744	0.2466	1.4631	0.0577	-0.0063	0.0544	-0.0603	-0.0213	-0.0226	0.1091	-0.0414	-0.0364	0.0531	-0.0024	-0.0048	0.0302	0.0038	0.0206	63.0156	34.6633	-16.1078
29	1.4764	-0.041	-0.6468	1.5787	0.1848	1.6453	0.0569	0.0045	-0.1405	-0.0559	-0.0313	0.0544	0.0979	0.0023	-0.0256	0.0624	0.0167	-0.0166	-0.014	-0.0012	0.0271	67.8439	22.8754	-9.0477
30	3.3644	0.0889	1.8012	0.0357	-0.6409	15.1744	-0.005	-0.1442	-0.07	-0.0872	0.0842	-0.0193	0.4386	-0.0404	-0.0792	0.0275	0.0164	-0.0173	0.0174	-0.0018	0.0082	72.1192	29.5019	10.0388

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 - 19	1 - 19
2	X-RAY DIFFRACTION	2	A	A	20 - 41	20 - 41
3	X-RAY DIFFRACTION	3	A	A	42 - 96	42 - 96
4	X-RAY DIFFRACTION	4	A	A	97 - 108	97 - 108
5	X-RAY DIFFRACTION	5	A	A	109 - 116	109 - 116
6	X-RAY DIFFRACTION	6	A	A	117 - 129	117 - 129
7	X-RAY DIFFRACTION	7	A	A	130 - 143	130 - 143
8	X-RAY DIFFRACTION	8	A	A	144 - 160	144 - 160
9	X-RAY DIFFRACTION	9	A	A	161 - 178	161 - 178
10	X-RAY DIFFRACTION	10	A	A	179 - 197	179 - 197
11	X-RAY DIFFRACTION	11	A	A	198 - 217	198 - 217
12	X-RAY DIFFRACTION	12	A	A	218 - 238	218 - 238
13	X-RAY DIFFRACTION	13	A	A	239 - 260	239 - 260
14	X-RAY DIFFRACTION	14	A	A	261 - 290	261 - 290
15	X-RAY DIFFRACTION	15	A	A	291 - 298	291 - 298
16	X-RAY DIFFRACTION	16	B	B	1 - 7	1 - 7
17	X-RAY DIFFRACTION	17	B	B	8 - 34	8 - 34
18	X-RAY DIFFRACTION	18	B	B	35 - 49	35 - 49
19	X-RAY DIFFRACTION	19	B	B	50 - 75	50 - 75
20	X-RAY DIFFRACTION	20	B	B	76 - 96	76 - 96
21	X-RAY DIFFRACTION	21	B	B	97 - 108	97 - 108
22	X-RAY DIFFRACTION	22	B	B	109 - 116	109 - 116
23	X-RAY DIFFRACTION	23	B	B	117 - 143	117 - 143
24	X-RAY DIFFRACTION	24	B	B	144 - 161	144 - 161
25	X-RAY DIFFRACTION	25	B	B	162 - 182	162 - 182
26	X-RAY DIFFRACTION	26	B	B	183 - 197	183 - 197
27	X-RAY DIFFRACTION	27	B	B	198 - 217	198 - 217
28	X-RAY DIFFRACTION	28	B	B	218 - 267	218 - 267
29	X-RAY DIFFRACTION	29	B	B	268 - 288	268 - 288
30	X-RAY DIFFRACTION	30	B	B	289 - 296	289 - 296

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