PDB-3dv9: Putative beta-phosphoglucomutase from Bacteroides vulgatus.

ID or keywords:

Entry

Database: PDB / ID: 3dv9

Title

Putative beta-phosphoglucomutase from Bacteroides vulgatus.

Components

beta-phosphoglucomutase

Keywords

ISOMERASE /

structural genomics / APC60149 /

beta-phosphoglucomutase / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity /

metal ion binding
Similarity search - Function

Biological species

Bacteroides vulgatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.72 Å

Authors

Osipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of putative beta-phosphoglucomutase from Bacteroides vulgatus.
Authors: Osipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Jul 18, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dv9.cif.gz	69 KB	Display	PDBx/mmCIF format
PDB format	pdb3dv9.ent.gz	57.1 KB	Display	PDB format
PDBx/mmJSON format	3dv9.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/dv/3dv9 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dv9	HTTPS FTP

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Related structure data

Similar structure data	6xab-d 6upd-2 3ouk-d 5tf8-d 2fea-2 6upb-1 3hx3-d 5uxv-2 3otv-4 3fmv-8 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: APC60149

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (4)

Deposited unit

A: beta-phosphoglucomutase

hetero molecules

28.1 kDa, 1 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)	64.247, 100.161, 38.991
Angle α, β, γ (deg.)	90.000, 97.820, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-308- HOH
2	1	A-333- HOH
3	1	A-400- HOH
4	1	A-479- HOH

Details

putative biological unit is the same as asym.

#1: Protein	beta-phosphoglucomutase / Mass: 27898.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_4110 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L7P8
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.23 Å³/Da / Density % sol: 44.78 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M magnesium formate, 15% PEG-3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Jul 12, 2008
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.72→26.9 Å / Num. all: 25739 / Num. obs: 25739 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / B_iso Wilson estimate: 31.1 Å² / R_merge(I) obs: 0.093 / Net I/σ(I): 28.9
Reflection shell	Resolution: 1.72→1.75 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.576 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1296 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.006	data extraction
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: 1.72→26.9 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.946 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.348 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1312	5.1 %	RANDOM
R_work	0.169	-	-	-
all	0.171	25732	-	-
obs	0.171	25732	99.34 %	-

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 max: 52.15 Å² / B_iso mean: 24.153 Å² / B_iso min: 10.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.13 Å²	0 Å²	0.25 Å²
2-	-	-0.43 Å²	0 Å²
3-	-	-	-0.63 Å²

Refinement step

Cycle: LAST / Resolution: 1.72→26.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1896	0	10	239	2145

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2082
X-RAY DIFFRACTION	r_angle_refined_deg	1.477	1.963	2832
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.592	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.24	25.051	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.305	15	375
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.018	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	306
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1596
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1021
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	1391
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	194
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.211	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.233	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	0.808	1.5	1319
X-RAY DIFFRACTION	r_mcangle_it	1.284	2	2064
X-RAY DIFFRACTION	r_scbond_it	2.042	3	854
X-RAY DIFFRACTION	r_scangle_it	3.168	4.5	753

LS refinement shell

Resolution: 1.72→1.765 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	93	-
R_work	0.239	1702	-
all	-	1795	-
obs	-	1795	94.23 %

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	5.6319	8.25	1.2267	13.7509	-1.5126	15.3778	-0.3464	-0.0452	-0.5632	0.1896	-0.0735	-1.4702	1.2324	1.197	0.4199	0.116	-0.0256	0.0409	-0.0076	0.0044	0.138	19.2718	68.502	10.9226
2	2.6909	-2.0391	1.4205	1.7943	-1.315	1.9938	0.079	-0.0283	-0.0275	0.1716	0.0028	0.1429	0.2929	-0.1245	-0.0818	-0.008	-0.0826	0.0211	-0.0779	0.0021	-0.0487	8.2408	70.6742	9.684
3	1.9129	1.3864	0.991	1.5158	1.1417	1.0682	0.0076	0.0535	0.1435	-0.017	-0.0417	0.1598	-0.0711	-0.1029	0.0341	-0.0692	-0.0063	-0.0052	-0.0218	0.0036	-0.0774	15.3768	84.4593	5.4676
4	1.5879	-1.2605	-0.9829	6.0887	0.8494	0.6094	0.0108	0.2645	-0.1072	0.1436	-0.1179	0.2065	-0.113	-0.1287	0.1071	0.0592	0.0422	-0.0256	-0.0565	-0.0037	-0.0448	17.26	104.949	25.0693
5	6.1012	0.869	-1.4019	3.1296	0.8795	0.7096	-0.1846	-0.1156	-0.112	0.2092	0.0877	0.4654	0.1873	0.1992	0.0969	-0.0147	0.023	-0.021	-0.0544	-0.0478	-0.0488	9.661	99.573	21.1627
6	1.2761	1.4576	-2.4834	3.5388	-2.1303	5.0992	-0.1998	-0.1823	-0.0561	0.197	0.0836	0.7648	0.3202	-0.4319	0.1161	0.2792	0.0323	0.0897	0.0552	-0.0373	0.335	1.8535	107.8914	26.2483
7	7.9824	-0.1962	-1.5352	6.4298	-0.1288	1.9953	-0.1396	0.3816	0.1485	-0.5151	-0.0745	0.5694	-0.3593	-0.1308	0.2141	0.1213	0.0531	-0.0681	-0.1592	-0.0055	-0.0548	7.6398	113.7795	18.6326
8	26.9345	-11.283	-10.4543	7.6835	5.989	7.5971	0.5293	0.9232	0.356	-0.663	-0.3852	-0.7286	-0.4397	-0.0362	-0.1441	0.1424	0.0308	0.0634	-0.1932	0.0176	-0.0621	21.6236	109.189	15.4887
9	4.3497	3.7161	3.6568	4.9595	3.6927	3.2555	0.0079	-0.1716	-0.0649	0.145	-0.0304	-0.0804	0.0534	-0.1473	0.0225	-0.0594	0.0183	-0.0048	-0.0477	0.0004	-0.0764	29.358	89.6761	7.093
10	2.3796	2.5374	2.0301	2.7056	2.1647	1.7319	-0.11	0.165	0.0351	0.0757	0.2093	-0.056	0.0527	-0.2058	-0.0993	-0.0668	0.009	-0.0002	-0.0329	0.0001	-0.0933	24.0415	82.1095	-3.1324
11	8.715	-2.0365	-3.5414	3.8631	7.3401	14.1301	0.0436	-0.258	1.0552	-0.5464	-0.0779	0.4052	-1.1308	0.0106	0.0343	0.0384	-0.004	-0.0151	-0.0002	0.0072	0.0624	16.4923	94.9007	4.1441
12	34.1692	14.7222	-30.7331	43.8772	7.8692	42.5849	1.4246	0.8459	2.6437	0.7384	-0.3997	2.7046	-3.1333	-0.3665	-1.0249	0.1415	0.0285	0.0578	0.0459	0.0829	0.1837	24.9645	100.5389	1.2253
13	6.4693	4.6508	-4.0604	11.2859	-0.1096	3.5423	-0.1423	0.4937	0.3205	-0.1849	0.1055	0.5904	-0.2863	-0.1935	0.0367	-0.0462	-0.0069	0.0054	-0.0162	0.0345	-0.073	25.0593	95.0514	-0.8235
14	23.4955	-5.6826	-18.4563	11.5061	23.3899	79.077	1.0183	1.4104	2.1127	-0.6315	0.0973	-1.3198	-2.0323	-0.0705	-1.1156	0.1686	0.0783	-0.0108	0.0886	0.1246	0.2493	13.1985	96.8151	0.3851
15	10.2659	1.7703	1.2157	8.0249	-8.3221	18.3698	0.0713	0.6349	0.9784	-0.9275	0.3533	0.1082	-1.9115	-0.8107	-0.4246	0.469	0.0858	-0.0202	0.1486	0.0213	0.2914	5.7299	99.2118	7.4099
16	1.5336	-1.0684	-0.8708	4.1326	3.4253	6.5409	0.0257	0.1908	0.3586	-0.1763	-0.0819	0.1967	-0.2181	-0.3397	0.0562	-0.1182	-0.0084	-0.0432	0.0071	0.0203	-0.034	6.4849	89.2841	2.7324
17	0.5637	0.1075	-0.1919	0.2023	-0.303	0.4556	-0.0073	-0.0146	-0.0096	0.0286	0.0085	0.0583	0.0213	-0.0355	-0.0012	-0.0655	-0.0078	-0.0048	-0.0461	-0.0095	-0.0595	13.4741	84.7579	13.2297
18	3.7923	-0.286	-0.4499	0.0219	0.0186	0.9046	-0.035	-0.0666	0.0367	0.0209	0.0474	-0.0301	0.0986	0.0064	-0.0125	-0.0447	-0.0125	-0.0051	-0.0478	0.0002	-0.0736	17.3173	81.0049	18.3338
19	0.1659	-0.6199	-0.8643	2.3165	3.23	4.5038	0.0121	-0.2541	-0.2869	0.0439	0.0287	-0.1325	0.1017	0.0733	-0.0408	-0.0435	0.01	-0.0091	-0.0658	0.0194	-0.0412	25.5967	77.2415	7.749
20	37.3544	-1.8348	2.5423	1.7653	-3.6219	7.6963	0.0383	1.7802	-1.3269	-1.2235	0.36	0.0357	0.5122	-0.0464	-0.3983	0.1686	-0.0318	0.0034	0.0896	-0.075	0.0876	17.9426	71.1633	0.6808

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	-2 - 3	1 - 6
2	X-RAY DIFFRACTION	2	A	A	4 - 12	7 - 15
3	X-RAY DIFFRACTION	3	A	A	13 - 34	16 - 37
4	X-RAY DIFFRACTION	4	A	A	35 - 57	38 - 60
5	X-RAY DIFFRACTION	5	A	A	58 - 73	61 - 76
6	X-RAY DIFFRACTION	6	A	A	74 - 84	77 - 87
7	X-RAY DIFFRACTION	7	A	A	85 - 90	88 - 93
8	X-RAY DIFFRACTION	8	A	A	91 - 103	94 - 106
9	X-RAY DIFFRACTION	9	A	A	104 - 115	107 - 118
10	X-RAY DIFFRACTION	10	A	A	116 - 122	119 - 125
11	X-RAY DIFFRACTION	11	A	A	123 - 135	126 - 138
12	X-RAY DIFFRACTION	12	A	A	136 - 140	139 - 143
13	X-RAY DIFFRACTION	13	A	A	141 - 149	144 - 152
14	X-RAY DIFFRACTION	14	A	A	150 - 155	153 - 158
15	X-RAY DIFFRACTION	15	A	A	156 - 162	159 - 165
16	X-RAY DIFFRACTION	16	A	A	163 - 179	166 - 182
17	X-RAY DIFFRACTION	17	A	A	180 - 211	183 - 214
18	X-RAY DIFFRACTION	18	A	A	212 - 228	215 - 231
19	X-RAY DIFFRACTION	19	A	A	229 - 237	232 - 240
20	X-RAY DIFFRACTION	20	A	A	238 - 243	241 - 246

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