PDB-3s30: Crystal structure of a putative glycoside hydrolase (BVU_0247) fr...

ID or keywords:

Entry

Database: PDB / ID: 3s30

Title

Crystal structure of a putative glycoside hydrolase (BVU_0247) from Bacteroides vulgatus ATCC 8482 at 2.46 A resolution

Components

Hypothetical glycoside hydrolase

Keywords

HYDROLASE / Galactose-binding domain-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY

Function / homology

BT2081, beta-jelly-roll domain / Putative carbohydrate metabolism domain / Putative carbohydrate metabolism domain superfamily / Putative carbohydrate metabolism domain / Jelly Rolls / Sandwich / Mainly Beta / PCMD domain-containing protein

Function and homology information

Biological species

Bacteroides vulgatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.46 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of a Hypothetical glycoside hydrolase (BVU_0247) from Bacteroides vulgatus ATCC 8482 at 2.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	May 17, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 8, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 20, 2011	Group: Structure summary
Revision 1.3	Nov 16, 2011	Group: Structure summary
Revision 1.4	Dec 24, 2014	Group: Structure summary
Revision 1.5	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.7	Feb 1, 2023	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s30.cif.gz	217.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3s30.ent.gz	177.5 KB	Display	PDB format
PDBx/mmJSON format	3s30.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3s30_validation.pdf.gz	441.7 KB	Display	wwPDB validaton report
Full document	3s30_full_validation.pdf.gz	443.6 KB	Display
Data in XML	3s30_validation.xml.gz	20.9 KB	Display
Data in CIF	3s30_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s3/3s30 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/3s30	HTTPS FTP

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Related structure data

Similar structure data	3uhp-1 2aqd-d 1ds4-d 5i9l-d 2vnk-4 4oq7-d 2cep-d 2as6-d 1qfj-1 4nko-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 - HomologyF&H Search
Other databases	TargetDB: 393205

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical glycoside hydrolase

B: Hypothetical glycoside hydrolase

hetero molecules

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

1

A: Hypothetical glycoside hydrolase

hetero molecules

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

2

B: Hypothetical glycoside hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	146.745, 146.745, 91.510
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	125 - 378
2	1	1	4	B	125 - 378

#1: Protein	Hypothetical glycoside hydrolase Mass: 39563.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_0247 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6KX05
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CONSTRUCT (RESIDUES 30-382) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 30-382) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.59 Å³/Da / Density % sol: 65.78 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 20.0% polyethylene glycol 3350, 0.2M ammonium nitrate, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.97874

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)

Radiation

Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97874 Å / Relative weight: 1

Reflection

Resolution: 2.46→29.656 Å / Num. obs: 40478 / % possible obs: 99.1 % / Redundancy: 4.2 % / R_merge(I) obs: 0.094 / R_sym value: 0.094 / Net I/σ(I): 12.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.46-2.52	4.2	0.811	0.9	12540	2977	0.811	98.7
2.52-2.59	4.2	0.664	1.2	12105	2873	0.664	98.9
2.59-2.67	4.2	0.562	1.3	11943	2835	0.562	98.8
2.67-2.75	4.2	0.427	1.8	11476	2726	0.427	98.8
2.75-2.84	4.2	0.374	2	11078	2635	0.374	98.8
2.84-2.94	4.2	0.289	2.6	10911	2593	0.289	98.9
2.94-3.05	4.2	0.218	3.5	10404	2467	0.218	98.8
3.05-3.18	4.2	0.162	4.7	10063	2401	0.162	99.4
3.18-3.32	4.2	0.126	6	9663	2294	0.126	99.3
3.32-3.48	4.2	0.095	7.7	9159	2185	0.095	99.4
3.48-3.67	4.2	0.081	8.9	8948	2130	0.081	99.1
3.67-3.89	4.2	0.069	6.8	8179	1957	0.069	99.6
3.89-4.16	4.2	0.059	10.5	7835	1874	0.059	99.4
4.16-4.49	4.2	0.049	13.1	7282	1746	0.049	99.7
4.49-4.92	4.2	0.045	14.4	6744	1622	0.045	99.7
4.92-5.5	4.1	0.048	13.8	6023	1453	0.048	99.8
5.5-6.35	4.1	0.056	12	5375	1298	0.056	99.9
6.35-7.78	4.1	0.052	12.9	4495	1096	0.052	100
7.78-11	4	0.047	13	3440	854	0.047	99.9
11-29.661	3.8	0.043	14	1748	462	0.043	94.7

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
MolProbity	3beta29	model building
PDB_EXTRACT	3.1	data extraction
SHELX		phasing
SHARP		phasing
SCALA	3.2.5	data scaling
REFMAC	5.5.0110	refinement
MOSFLM		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.46→29.656 Å / Cor.coef. F_o:F_c: 0.913 / Cor.coef. F_o:F_c free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.866 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2506	2033	5 %	RANDOM
R_work	0.2325	-	-	-
obs	0.2334	40475	99.21 %	-

Solvent computation

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

Displacement parameters

B_iso max: 126.85 Å² / B_iso mean: 63.9867 Å² / B_iso min: 37.85 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.46 Å²	0.23 Å²	0 Å²
2-	-	0.46 Å²	0 Å²
3-	-	-	-0.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.46→29.656 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3972	0	2	168	4142

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4075
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2667
X-RAY DIFFRACTION	r_angle_refined_deg	1.134	1.949	5536
X-RAY DIFFRACTION	r_angle_other_deg	0.799	3	6525
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.274	5	510
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.569	25.08	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.291	15	641
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.535	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	601
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	4607
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	841
X-RAY DIFFRACTION	r_mcbond_it	1.003	3	2524
X-RAY DIFFRACTION	r_mcbond_other	0.27	3	1049
X-RAY DIFFRACTION	r_mcangle_it	1.812	5	4064
X-RAY DIFFRACTION	r_scbond_it	3.563	8	1551
X-RAY DIFFRACTION	r_scangle_it	4.659	11	1471

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3296 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
MEDIUM POSITIONAL	0.28	0.5
MEDIUM THERMAL	0.47	2

LS refinement shell

Resolution: 2.46→2.524 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	134	-
R_work	0.273	2830	-
all	-	2964	-
obs	-	-	98.77 %

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	2.7127	1.0814	1.7947	8.4073	7.5209	5.6099	-0.2505	0.186	0.4619	-0.8912	0.1197	0.3027	-0.7212	0.1215	0.1308	0.3085	0.0301	-0.0134	0.3115	0.053	0.3222	3.7885	44.4198	-2.3967
2	4.0258	-0.6024	-0.2778	2.4072	-1.0932	3.2618	0.0824	0.2254	-0.1673	-0.1278	-0.1306	0.2319	0.1374	-0.1988	0.0481	0.2111	-0.0249	-0.0452	0.2232	0.0104	0.141	9.0221	33.3704	-6.2016
3	20.5406	-11.5104	-3.9181	2.0817	6.1693	33.8073	0.2721	0.5406	0.2547	-0.0926	-0.0637	-0.0552	0.4018	0.5149	-0.2084	0.439	0.0526	0.0911	0.4421	-0.0249	0.2028	26.291	24.7552	-12.7974
4	0.5853	0.1417	0.5349	3.3026	-0.0642	2.8855	0.1178	0.2768	0.1817	-0.4708	0.0345	-0.2629	-0.2108	0.2954	-0.1523	0.251	-0.0133	0.0555	0.2762	0.0373	0.2363	19.3533	42.1035	-7.5408
5	4.6905	-1.3062	-0.6715	6.9044	0.1835	2.8226	0.0193	-0.1141	-0.1291	-0.1049	-0.0059	0.1871	-0.0072	0.1112	-0.0134	0.1839	-0.0729	-0.0613	0.2547	0.0119	0.005	18.5865	34.7733	6.8716
6	6.9894	-12.4175	1.1676	24.8303	-0.2543	-1.0306	0.0322	0.0534	-0.0026	0.1613	0.023	-0.2794	0.0489	0.0861	-0.0552	0.2653	0.0289	-0.0196	0.2697	0.0305	0.2673	27.0896	24.431	7.4242
7	3.1915	-0.0176	0.5958	4.3076	0.7512	2.0081	0.0636	0.0692	0.4418	-0.024	-0.1772	-0.5822	-0.5453	0.5739	0.1137	0.2616	-0.0984	0.0194	0.316	0.0483	0.2935	24.0964	48.7858	1.1695
8	3.3738	2.3068	-1.0321	8.8651	-1.3245	2.5027	0.1625	-0.244	0.4013	0.7081	-0.0251	-0.2316	-0.4	0.1739	-0.1374	0.2998	-0.0209	-0.0163	0.3117	-0.0119	0.1813	17.7348	44.7995	12.4344
9	2.3233	0.0496	-0.181	3.8078	-0.4488	2.3666	0.0941	-0.0756	0.4908	0.025	-0.0157	-0.0845	-0.4347	0.0668	-0.0783	0.2636	-0.0502	-0.0097	0.2623	0.0016	0.1748	16.7666	45.2386	2.3534
10	2.6546	-0.6103	-0.8798	5.3145	-3.1887	2.2416	0.2499	-0.3209	0.5592	0.5488	-0.2839	-0.5459	-0.4424	0.4915	0.034	0.269	-0.0688	-0.0259	0.3978	-0.0575	0.2988	12.5499	44.8181	40.3985
11	4.0385	0.341	-0.0937	2.5759	0.5943	3.6961	0.0345	-0.2708	-0.239	0.1144	-0.0702	-0.2167	0.2684	0.2195	0.0357	0.2253	0.0309	-0.0398	0.2115	-0.0031	0.1515	2.9524	34.3956	43.3706
12	11.5367	-1.7874	-3.364	13.5956	-6.79	28.8441	-0.4284	-0.2857	0.5897	0.5265	0.4369	0.2179	-0.1786	-0.3892	-0.0085	0.3627	-0.0271	0.1142	0.523	-0.0156	0.1744	-16.252	32.218	49.9479
13	1.8097	0.9651	0.8167	3.2978	-0.3446	2.9136	0.1773	-0.3386	0.4472	0.393	-0.0314	0.2339	-0.3275	-0.1506	-0.1459	0.2589	-0.0096	0.0615	0.2471	-0.0799	0.2491	-3.7408	46.1552	44.7064
14	4.1032	0.7559	-0.3799	4.4302	0.4552	2.9511	-0.0391	0.1498	0.1547	-0.0647	0.0543	0.1119	0.0279	-0.0859	-0.0153	0.2333	0.0749	-0.08	0.2241	0.0344	0.043	-5.5359	38.9977	30.3083
15	18.4858	11.8983	0.0097	7.2635	-0.84	1.8414	-0.1391	0.3035	-0.0481	-0.1096	0.1126	-0.0264	0.1912	-0.1775	0.0265	0.2213	-0.0052	-0.0299	0.2806	-0.0389	0.2937	-17.116	32.2215	29.7712
16	2.8567	-0.4278	-0.257	2.4872	-1.1392	1.9761	0.1324	-0.0743	0.8045	-0.0126	-0.1506	0.2863	-0.6458	-0.3004	0.0183	0.3943	0.1067	-0.032	0.276	-0.0542	0.4436	-5.8789	54.0656	35.8619
17	2.7976	0.4016	-0.357	9.2703	1.4051	2.8117	0.0902	0.2538	0.5468	-0.6479	0.0649	-0.0155	-0.51	-0.1188	-0.1551	0.3273	-0.0068	-0.0165	0.3373	0.0658	0.2183	-1.1726	48.4413	24.6646
18	2.6823	1.0083	-0.24	3.5337	0.1713	2.515	0.0956	0.0994	0.6231	0.0013	-0.0003	-0.0356	-0.4406	0.1286	-0.0953	0.2898	0.0271	-0.008	0.2363	0.0427	0.2252	-0.186	48.1433	34.7961

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	125 - 140
2	X-RAY DIFFRACTION	2	A	141 - 202
3	X-RAY DIFFRACTION	3	A	203 - 212
4	X-RAY DIFFRACTION	4	A	213 - 243
5	X-RAY DIFFRACTION	5	A	244 - 266
6	X-RAY DIFFRACTION	6	A	267 - 273
7	X-RAY DIFFRACTION	7	A	274 - 313
8	X-RAY DIFFRACTION	8	A	314 - 334
9	X-RAY DIFFRACTION	9	A	335 - 378
10	X-RAY DIFFRACTION	10	B	123 - 140
11	X-RAY DIFFRACTION	11	B	141 - 202
12	X-RAY DIFFRACTION	12	B	203 - 212
13	X-RAY DIFFRACTION	13	B	213 - 243
14	X-RAY DIFFRACTION	14	B	244 - 266
15	X-RAY DIFFRACTION	15	B	267 - 273
16	X-RAY DIFFRACTION	16	B	274 - 313
17	X-RAY DIFFRACTION	17	B	314 - 334
18	X-RAY DIFFRACTION	18	B	335 - 378

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi