PDB-3uny: Bacillus cereus phosphopentomutase T85E variant soaked with gluco...

ID or keywords:

Entry

Database: PDB / ID: 3uny

Title

Bacillus cereus phosphopentomutase T85E variant soaked with glucose 1,6-bisphosphate

Components

Phosphopentomutase

Keywords

ISOMERASE / alkaline phosphatase family

Function / homology

Function and homology information

metabolic compound salvage / phosphopentomutase / phosphopentomutase activity / 2-deoxyribose 1-phosphate catabolic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleotide metabolic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 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 16, 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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PDBx/mmCIF format	3uny.cif.gz	940.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3uny_validation.pdf.gz	488.8 KB	Display	wwPDB validaton report
Full document	3uny_full_validation.pdf.gz	510 KB	Display
Data in XML	3uny_validation.xml.gz	99.4 KB	Display
Data in CIF	3uny_validation.cif.gz	143.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/un/3uny ftp://data.pdbj.org/pub/pdb/validation_reports/un/3uny	HTTPS FTP

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Related structure data

Related structure data	3twzC 3tx0C 3un2C 3un3C 3un5C 3uo0C C: citing same article (ref.)
Similar structure data	3un5-2 4lrf-3 3un5-4 4lra-1 4lra-2 4lr9-1 4lre-3 3m8w-2 4lr7-1 3m8z-3 3un5-5 3un2-2 4lrb-2 3twz-d 3m8y-3 4gxt-d 4lrc-3 4lre-1 4lrb-3 4lrb-1 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

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

1

A: Phosphopentomutase

hetero molecules

defined by author&software
44.7 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)	106.582, 76.791, 182.287
Angle α, β, γ (deg.)	90.00, 106.07, 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.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1839 / 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: 2.68 Å³/Da / Density % sol: 54.14 %
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, soaked with 5 mM glucose 1,6-bisphosphate, 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: 1.95→20 Å / Num. all: 208069 / Num. obs: 206406 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 1.95→2.01 Å / % possible all: 95.9

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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: 1.95→20 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.494 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19919	10161	5 %	RANDOM
R_work	0.16687	-	-	-
obs	0.16849	194503	99.29 %	-

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: 22.564 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.54 Å²	0 Å²	0.75 Å²
2-	-	-1.2 Å²	0 Å²
3-	-	-	1.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18372	0	34	1839	20245

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	18745
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.101	1.985	25320
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.538	5	2343
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.725	25.109	875
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.765	15	3338
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.922	15	91
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	2760
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	14259
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	0.368	1.5	11625
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.733	2	18724
X-RAY DIFFRACTION	r_scbond_it	1.467	3	7120
X-RAY DIFFRACTION	r_scangle_it	2.476	4.5	6596
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.241	663	-
R_work	0.216	13774	-
obs	-	-	95.91 %

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	1.836	0.2592	0.4649	1.99	-0.0037	1.7506	0.0033	-0.0804	-0.0014	0.2033	0.0192	0.3664	0.0554	-0.326	-0.0225	0.0369	0.0039	0.0454	0.0788	0.0041	0.09	-39.6851	-18.2598	89.9093
2	1.3421	-0.2945	-1.7759	0.203	0.2391	4.5718	-0.0355	0.3417	0.0093	-0.1394	-0.0789	0.0376	0.0124	-0.1397	0.1143	0.1813	-0.0344	-0.0358	0.1338	0.0301	0.0988	-25.3063	-6.031	65.5542
3	5.7269	-3.8758	-2.1962	6.217	2.3926	4.0175	-0.0727	-0.019	0.0495	0.093	-0.0203	-0.1039	0.1324	0.2553	0.093	0.0858	-0.0254	-0.0081	0.1076	0.0487	0.0238	-15.1522	-8.3923	64.7856
4	1.4852	0.3358	0.5024	2.1882	0.0603	1.2762	0.0046	-0.0224	-0.0183	0.1908	0.026	-0.0339	-0.0314	0.0629	-0.0305	0.0235	0.0044	0.0049	0.0075	0.0025	0.0097	-26.9723	-14.9173	90.2438
5	5.3301	1.0732	-3.8936	1.4914	-0.6142	4.3044	0.2845	-0.6593	0.0121	0.2741	-0.2284	-0.0638	-0.228	0.3198	-0.0562	0.1241	-0.0304	-0.0412	0.2377	0.0667	0.053	0.9765	8.7924	43.1265
6	2.4893	0.1115	-0.5096	2.8085	-1.0554	2.0284	0.0474	-0.6013	-0.2937	0.2691	-0.149	-0.1446	-0.0385	0.2978	0.1016	0.1396	-0.0483	-0.0367	0.322	0.0782	0.0731	2.5426	5.1434	45.281
7	3.2777	0.3305	0.4496	2.0809	0.399	5.3826	0.0468	-0.1879	-0.0104	0.1309	-0.0159	0.0937	-0.0912	-0.4061	-0.0309	0.0343	0.0386	0.0057	0.1207	0.0329	0.0805	-23.4522	8.6737	23.9012
8	2.8775	0.7887	-1.4241	1.3797	-0.7802	1.9409	-0.0127	-0.303	-0.2096	0.0139	-0.1182	-0.1729	-0.0129	0.2165	0.1309	0.0754	-0.0006	-0.0481	0.1399	0.049	0.0728	5.3361	7.6473	34.2647
9	1.6548	-0.3262	-0.2551	1.8694	-0.1906	1.4146	-0.089	-0.2747	-0.0803	0.4406	0.0755	0.0585	0.0603	-0.0272	0.0134	0.1575	-0.0021	0.0017	0.0722	-0.0049	0.0406	-0.4246	-30.7408	12.8616
10	2.5386	0.7101	2.5205	1.0662	0.9781	4.6847	-0.0035	-0.3792	0.1643	0.1011	-0.1748	0.3465	-0.1156	-0.8406	0.1783	0.1085	0.028	0.0527	0.2682	-0.0024	0.2491	-27.2169	-20.607	-2.8812
11	3.1304	1.3203	1.199	2.9156	1.273	5.4099	-0.0003	0.0323	-0.0998	-0.0751	-0.0391	0.0531	0.0855	-0.2948	0.0394	0.0257	0.013	0.0122	0.078	0.0063	0.1207	-23.5892	-23.7755	-11.3952
12	1.3274	-0.1844	-0.5206	1.8254	-0.2058	1.4304	-0.0382	0.0016	0.0098	0.1019	0.0349	-0.0115	0.0465	0.0169	0.0034	0.0403	-0.0017	-0.0143	0.0043	-0.0062	0.0313	2.4827	-30.498	2.1658
13	1.8965	-0.1851	-0.549	1.1622	0.03	1.9651	-0.0656	-0.4456	-0.1456	0.3504	0.0642	0.0021	0.1049	0.0591	0.0013	0.1407	0.014	-0.0226	0.1243	0.0179	0.0547	28.9241	-31.1133	102.5816
14	4.2974	0.6117	1.9865	0.1471	0.3779	1.398	0.0305	-0.2299	0.0829	0.0422	-0.0656	0.0748	0.0069	-0.3211	0.0351	0.0919	0.0111	0.0263	0.1199	0.0079	0.1241	5.992	-18.3828	86.1964
15	3.3771	1.1829	0.7402	3.6083	2.214	4.4154	0.0023	0.1019	-0.0986	-0.0354	-0.0231	-0.1118	0.0281	-0.0389	0.0208	0.0117	0.0242	0.0174	0.0735	0.0298	0.0605	5.8372	-20.779	75.7267
16	1.5068	-0.1625	-0.5452	1.4916	-0.1978	1.4121	-0.0341	0.0041	0.0063	0.0316	0.0364	-0.0471	0.0285	0.0411	-0.0023	0.0175	0.0043	-0.0218	0.0109	-0.0078	0.0293	30.7194	-27.5329	89.6659
17	4.0697	0.2158	-1.7183	1.2512	0.1047	2.319	-0.0906	0.8618	-0.4694	-0.2434	-0.0145	0.0977	0.0922	-0.3426	0.1051	0.102	-0.0057	-0.0278	0.3456	-0.1117	0.1152	22.9136	-33.3544	41.7333
18	4.7438	-0.9931	2.4108	0.247	-0.3778	2.6596	0.1036	0.4216	0.059	-0.0358	-0.0626	-0.0823	0.0292	0.4114	-0.041	0.1169	-0.0418	0.0244	0.1944	-0.0184	0.1497	48.337	-25.0236	56.7612
19	4.7678	-0.2496	1.1192	6.0152	-1.6587	6.0825	-0.0258	0.1005	0.0235	-0.1113	0.055	0.1036	-0.0619	0.0292	-0.0292	0.0129	-0.0255	0.0162	0.0738	-0.0378	0.0417	48.0611	-26.424	67.0926
20	2.9428	-0.3643	-1.1739	1.079	0.6491	1.8415	-0.0617	0.2817	-0.1923	0.0181	-0.0081	0.0681	0.0393	-0.1464	0.0698	0.0456	-0.0013	-0.0089	0.1219	-0.0234	0.0611	22.196	-28.7354	53.656
21	1.7502	0.2127	0.4149	1.9973	-0.1306	1.8419	0.0029	-0.0857	-0.0067	0.1194	0.0504	0.322	0.0536	-0.3601	-0.0533	0.0493	0.001	0.0303	0.0923	0.0192	0.0997	38.7926	-16.3559	1.8463
22	1.825	0.0647	-2.3964	0.2419	-0.3887	5.0001	-0.1385	0.444	-0.0392	-0.1898	-0.0175	0.013	0.2794	-0.2841	0.156	0.1703	-0.0299	-0.0024	0.1588	0.0193	0.0789	54.0966	-4.2515	-22.1102
23	6.0151	-3.5522	-3.2791	5.7754	3.6159	8.3302	-0.2126	-0.0711	0.004	0.2725	0.1162	-0.1921	0.7091	0.7053	0.0964	0.1601	0.0372	0.0263	0.146	0.0509	0.0412	64.5772	-5.7297	-22.706
24	1.5761	0.41	0.3662	2.1435	-0.2525	1.2469	-0.0179	-0.0474	-0.0346	0.1345	0.0443	-0.0909	-0.0461	0.0419	-0.0265	0.0374	0.006	0.0125	0.0068	-0.0014	0.0158	51.2336	-13.0216	2.6676

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	2 - 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	2 - 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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