PDB-3un5: Bacillus cereus phosphopentomutase T85E variant

ID or keywords:

Entry

Database: PDB / ID: 3un5

Title

Bacillus cereus phosphopentomutase T85E variant

Components

Phosphopentomutase

Keywords

ISOMERASE /

alkaline phosphatase family

Function / homology

Function and homology information

phosphopentomutase /

phosphopentomutase activity / cellular metabolic compound salvage / 5-phosphoribose 1-diphosphate biosynthetic process / deoxyribonucleotide catabolic process / manganese ion binding / magnesium ion binding /

cytosol
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Iverson, T.M. / Birmingham, W.R. / Panosian, T.D. / Nannemann, D.P. / Bachmann, B.O.

Citation

Journal: Biochemistry / Year: 2012
Title: Molecular Differences between a Mutase and a Phosphatase: Investigations of the Activation Step in Bacillus cereus Phosphopentomutase.
Authors: Iverson, T.M. / Panosian, T.D. / Birmingham, W.R. / Nannemann, D.P. / Bachmann, B.O.

History

Deposition	Nov 15, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 21, 2012	Group: Database references
Revision 1.2	Jul 17, 2019	Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software Item: _software.classification / _software.name / _software.version
Revision 1.3	Feb 28, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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	3un5.cif.gz	932.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3un5.ent.gz	776.3 KB	Display	PDB format
PDBx/mmJSON format	3un5.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/un/3un5 ftp://data.pdbj.org/pub/pdb/validation_reports/un/3un5	HTTPS FTP

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Related structure data

Related structure data	3twzC 3tx0C 3un2C 3un3C 3unyC 3uo0C C: citing same article (ref.)
Similar structure data	3uo0-1 3uny-4 3tx0-d 3ot9-3 4lra-3 4lrb-3 4lr9-1 3m8w-1 4lr9-3 3uny-3 4lrf-3 4lr8-1 3uny-5 1hmy-d 4lra-1 6dpr-2 3un2-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (3)

Deposited unit

A: Phosphopentomutase

B: Phosphopentomutase

C: Phosphopentomutase

D: Phosphopentomutase

E: Phosphopentomutase

F: Phosphopentomutase

hetero molecules

269 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphopentomutase

hetero molecules

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

2

B: Phosphopentomutase

hetero molecules

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

3

C: Phosphopentomutase

hetero molecules

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

4

D: Phosphopentomutase

hetero molecules

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

5

E: Phosphopentomutase

hetero molecules

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

6

F: Phosphopentomutase

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.447, 76.829, 182.841
Angle α, β, γ (deg.)	90.00, 105.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphopentomutase / / Phosphodeoxyribomutase Mass: 44539.336 Da / Num. of mol.: 6 / Mutation: T85E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: deoB, BC_4087 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1864 / 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: 2.69 Å³/Da / Density % sol: 54.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Bis-Tris, pH 5.5, 50 mM manganese chloride, 17% PEG3350, 75 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2010
Radiation	Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.8→20 Å / Num. all: 261280 / Num. obs: 254487 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 1.8→1.86 Å / % possible all: 84.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
CNS		refinement
HKL-2000		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.552 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19281	12792	5 %	RANDOM
R_work	0.16669	-	-	-
obs	0.16802	241530	100 %	-
all	-	254487	-	-

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 mean: 21.652 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	0.79 Å²
2-	-	-0.88 Å²	0 Å²
3-	-	-	1.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18356	0	42	1864	20262

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	18910
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.032	1.985	25556
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.385	5	2371
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.33	25.045	888
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.803	15	3386
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.232	15	97
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	2773
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	14437
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.357	1.5	11705
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.733	2	18882
X-RAY DIFFRACTION	r_scbond_it	1.395	3	7205
X-RAY DIFFRACTION	r_scangle_it	2.417	4.5	6674
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.848 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	824	-
R_work	0.245	14608	-
obs	-	-	100 %

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	0.6033	0.1033	0.0492	1.0568	0.0639	0.7755	-0.006	-0.0468	0.0062	0.1372	-0.0091	0.2144	0.0221	-0.1485	0.0151	0.0197	-0.0011	0.0257	0.036	0.0022	0.0719	-39.6333	-18.3151	90.4746
2	0.9211	-0.2084	-0.5396	0.2811	0.1529	1.6168	-0.0139	0.2066	0.0473	-0.088	-0.045	0.0388	-0.0021	-0.0663	0.0589	0.0702	-0.0148	-0.0156	0.0569	0.0205	0.0303	-25.2519	-5.8262	65.6389
3	2.5818	-1.7504	-0.876	3.1924	0.909	1.7171	-0.0446	0.0353	0.0273	0.0108	-0.0424	-0.0059	0.0605	0.1465	0.087	0.0535	-0.0035	0.0026	0.0662	0.0263	0.0118	-15.2126	-8.2904	64.9618
4	0.4736	0.1021	0.1067	1.0614	0.0622	0.5823	0.0033	-0.0145	-0.0252	0.1013	0.0055	0.0018	-0.0198	0.0042	-0.0088	0.0232	0.0021	0	0.0183	-0.0005	0.0295	-26.9167	-14.8719	90.6029
5	2.8791	0.6986	-1.9431	0.443	-0.2333	1.9941	0.157	-0.4504	-0.0279	0.1666	-0.1624	-0.0722	-0.1054	0.2404	0.0055	0.1096	-0.0106	-0.0228	0.1948	0.0724	0.0493	1.3108	8.7272	43.0228
6	1.4336	0.3196	-0.6265	1.679	-0.3077	0.9842	0.0463	-0.4495	-0.1415	0.1848	-0.1443	-0.103	-0.0992	0.2218	0.098	0.0607	-0.0316	-0.0262	0.2203	0.0763	0.0309	2.3446	5.2705	45.3173
7	1.4665	0.1016	0.2249	1.0171	0.0651	2.4976	0.0317	-0.1106	-0.0561	0.0608	0.0004	0.0403	-0.0612	-0.2158	-0.0322	0.0228	0.0265	-0.0008	0.0646	0.0197	0.0364	-23.3966	8.6353	24.1909
8	1.6158	0.3538	-0.8827	0.7842	-0.3491	1.0786	-0.0248	-0.2761	-0.1904	0.0287	-0.0889	-0.129	-0.0089	0.172	0.1137	0.0287	-0.0069	-0.0195	0.0957	0.0554	0.0502	5.3213	7.5939	34.5005
9	0.7898	-0.0325	-0.0453	0.823	-0.1287	0.5858	-0.0312	-0.1505	0.0045	0.2455	0.0431	0.01	0.0145	-0.014	-0.0119	0.1057	0.0089	0.0076	0.0327	0.0002	0.0087	-0.4236	-30.7247	12.8423
10	1.3211	0.3814	1.6714	1.5597	0.9846	3.5191	0.03	-0.3438	0.0788	0.1554	-0.1749	0.2652	-0.0639	-0.6029	0.1449	0.039	0.0091	0.0506	0.1466	-0.0084	0.127	-27.2328	-20.5929	-3.017
11	1.5207	0.7236	0.3707	1.3259	0.3902	2.1018	0.0018	-0.0074	-0.0478	-0.0153	-0.0122	0.0751	-0.0472	-0.1818	0.0104	0.0027	0.0082	0.0027	0.0355	-0.0072	0.0752	-23.6374	-23.7974	-11.5128
12	0.4808	-0.0799	-0.1346	0.7445	0.0031	0.554	-0.0321	-0.0195	-0.002	0.0881	0.0235	-0.0029	0.0322	0.0021	0.0087	0.0436	-0.0072	-0.0028	0.009	-0.0021	0.0377	2.531	-30.4267	2.1347
13	0.8813	-0.0309	0.0113	0.7121	-0.1149	0.6986	-0.0283	-0.2039	-0.0547	0.1903	0.0476	-0.0353	0.0382	0.0273	-0.0193	0.075	0.0161	-0.017	0.0532	0.0095	0.0168	29.0622	-31.1025	102.8245
14	1.6296	0.3325	0.6867	0.2839	0.303	0.9227	0.0009	-0.1488	0.014	0.0267	-0.0361	0.0314	0.0025	-0.1908	0.0352	0.0185	0.0062	0.0085	0.0486	0.0011	0.0526	5.9867	-18.3924	86.4307
15	1.389	0.7327	0.3388	2.0288	0.9194	1.9939	0.0123	0.0094	-0.034	0.0003	-0.0283	-0.0466	-0.0079	-0.0441	0.016	0.0029	0.0082	0.0089	0.0428	0.0138	0.0422	5.9348	-20.6275	76.0404
16	0.4837	-0.1417	-0.1243	0.551	-0.0137	0.5156	-0.0329	-0.0215	-0.0004	0.0502	0.0292	-0.0209	0.0382	0.0106	0.0036	0.0199	-0.0021	-0.0124	0.0208	-0.0029	0.0496	30.5875	-27.6216	90.0068
17	2.0631	0.0108	-0.6337	0.6849	-0.0436	0.9323	-0.0348	0.519	-0.2576	-0.168	-0.0068	0.0743	0.042	-0.1775	0.0416	0.0459	-0.0151	-0.0118	0.2077	-0.0959	0.0545	23.0377	-33.7169	41.7632
18	1.9529	-0.4965	0.9654	0.426	-0.1097	1.5533	0.0755	0.3288	-0.0211	-0.0299	-0.0311	-0.0444	-0.0187	0.2597	-0.0444	0.0433	-0.0241	0.0168	0.1033	-0.0108	0.0432	48.4454	-24.993	56.9833
19	2.2798	-0.0093	0.4587	2.5287	-0.4869	2.8114	0.0029	0.0703	0.0212	-0.0199	0.0293	-0.0373	-0.0714	0.072	-0.0323	0.0058	-0.0127	0.0038	0.0429	-0.0198	0.0283	47.8442	-26.3331	67.2902
20	1.6733	-0.0655	-0.626	0.563	0.215	0.884	-0.0535	0.2174	-0.1438	0.012	-0.0119	0.047	0.0202	-0.0996	0.0654	0.0061	0.0035	-0.0003	0.0663	-0.0259	0.0269	22.0803	-28.7209	53.8597
21	0.8576	0.2566	0.1919	1.0027	0.0786	0.8894	-0.0133	-0.0181	-0.0087	0.0848	0.022	0.1932	0.0353	-0.1633	-0.0087	0.0422	-0.0038	0.0213	0.0419	0.0097	0.0548	38.2829	-16.6471	1.5989
22	1.2989	-0.068	-1.1011	0.1834	-0.1189	2.1577	-0.0737	0.2523	0.0164	-0.0704	-0.0144	-0.025	0.1722	-0.1817	0.0881	0.0983	-0.0231	0.0082	0.0628	0.0186	0.0232	53.9147	-4.0099	-22.0093
23	3.0608	-1.4071	-1.7918	2.5474	2.2325	4.3878	-0.1333	-0.0418	0.0215	0.1538	0.0969	-0.1541	0.4012	0.3992	0.0364	0.1074	0.0434	0.027	0.089	0.0312	0.0317	64.4425	-5.8793	-22.8523
24	0.5478	0.207	0.0285	1.0717	-0.1129	0.6607	-0.0096	-0.0105	-0.0369	0.0613	0.0153	-0.0357	-0.0082	0.001	-0.0057	0.0456	-0.0015	0.005	0.0207	-0.0014	0.0185	51.1651	-13.0615	2.6644

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 79
2	X-RAY DIFFRACTION	2	A	80 - 158
3	X-RAY DIFFRACTION	3	A	159 - 215
4	X-RAY DIFFRACTION	4	A	216 - 392
5	X-RAY DIFFRACTION	5	B	3 - 31
6	X-RAY DIFFRACTION	6	B	32 - 100
7	X-RAY DIFFRACTION	7	B	101 - 216
8	X-RAY DIFFRACTION	8	B	217 - 392
9	X-RAY DIFFRACTION	9	C	3 - 98
10	X-RAY DIFFRACTION	10	C	99 - 140
11	X-RAY DIFFRACTION	11	C	141 - 215
12	X-RAY DIFFRACTION	12	C	216 - 392
13	X-RAY DIFFRACTION	13	D	3 - 79
14	X-RAY DIFFRACTION	14	D	80 - 158
15	X-RAY DIFFRACTION	15	D	159 - 215
16	X-RAY DIFFRACTION	16	D	216 - 392
17	X-RAY DIFFRACTION	17	E	3 - 79
18	X-RAY DIFFRACTION	18	E	80 - 158
19	X-RAY DIFFRACTION	19	E	159 - 215
20	X-RAY DIFFRACTION	20	E	216 - 392
21	X-RAY DIFFRACTION	21	F	3 - 79
22	X-RAY DIFFRACTION	22	F	80 - 158
23	X-RAY DIFFRACTION	23	F	159 - 215
24	X-RAY DIFFRACTION	24	F	216 - 392

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