PDB-3ibx: Crystal structure of F47Y variant of TenA (HP1287) from Helicobac...

ID or keywords:

Entry

Database: PDB / ID: 3ibx

Title

Crystal structure of F47Y variant of TenA (HP1287) from Helicobacter pylori

Components

Putative thiaminase II

Keywords

HYDROLASE / Thiamin / Vitamin B1 / Helicobacter pylori / thiaminase

Function / homology

Function and homology information

aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytosol
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Barison, N. / Cendron, L. / Trento, A. / Angelini, A. / Zanotti, G.

Citation

Journal: Febs J. / Year: 2009
Title: Structural and mutational analysis of TenA protein (HP1287) from the Helicobacter pylori thiamin salvage pathway - evidence of a different substrate specificity.
Authors: Barison, N. / Cendron, L. / Trento, A. / Angelini, A. / Zanotti, G.

History

Deposition	Jul 17, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 10, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	3ibx_validation.pdf.gz	434.4 KB	Display	wwPDB validaton report
Full document	3ibx_full_validation.pdf.gz	441.7 KB	Display
Data in XML	3ibx_validation.xml.gz	17.3 KB	Display
Data in CIF	3ibx_validation.cif.gz	23.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/3ibx ftp://data.pdbj.org/pub/pdb/validation_reports/ib/3ibx	HTTPS FTP

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Related structure data

Related structure data	2rd3S 1to9 1tyh S: Starting model for refinement
Similar structure data	2rd3-1 2gm8-d 2gm7-d 6zt3-1 1rtw-d 6m5e-2 6vlx-1 5vh4-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative thiaminase II

D: Putative thiaminase II

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

1

A: Putative thiaminase II

D: Putative thiaminase II

A: Putative thiaminase II

D: Putative thiaminase II

defined by author&software
102 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	148.728, 148.728, 233.566
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D

#1: Protein	Putative thiaminase II / tenA / HP1287 Mass: 25510.930 Da / Num. of mol.: 2 / Mutation: F47Y Source method: isolated from a genetically manipulated source Details: Mutated with the QuikChange Site-directed mutagenesis kit (Stratagene) Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG17874 / Gene: tenA, HP1287 / Plasmid: pET151-HP1287 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A8KRL3, aminopyrimidine aminohydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative thiaminase II / tenA / HP1287

Mass: 25510.930 Da / Num. of mol.: 2 / Mutation: F47Y
Source method: isolated from a genetically manipulated source
Details: Mutated with the QuikChange Site-directed mutagenesis kit (Stratagene)
Source: (gene. exp.)

Helicobacter pylori (bacteria) / Strain: CCUG17874 / Gene: tenA, HP1287 / Plasmid: pET151-HP1287 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A8KRL3, aminopyrimidine aminohydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 64 / 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 grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, 1.1M lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.4→125 Å / Num. all: 51200 / Num. obs: 51200 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / R_merge(I) obs: 0.153 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 10.2 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7412 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2RD3

2rd3

Resolution: 2.4→78 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.925 / SU B: 10.122 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22957	2541	5.1 %	RANDOM
R_work	0.21771	-	-	-
obs	0.21831	50181	97.74 %	-
all	-	51200	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.875 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0 Å²	0 Å²
2-	-	0.38 Å²	0 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3553	0	0	64	3617

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3638
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.245	1.934	4927
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.556	5	434
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.632	24.944	180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.346	15	625
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.989	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2765
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	0.417	1.5	2171
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.853	2	3488
X-RAY DIFFRACTION	r_scbond_it	1.299	3	1467
X-RAY DIFFRACTION	r_scangle_it	2.119	4.5	1439
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 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
860	medium positional	0.25	0.5
888	loose positional	0.5	5
860	medium thermal	2.28	2
888	loose thermal	2.4	10

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	172	-
R_work	0.275	3543	-
obs	-	-	99.31 %

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	0.2719	0.3414	1.0799	4.239	-6.3879	20.132	0.054	-0.0128	-0.0531	-0.2792	0.1925	0.0079	1.1306	-0.4451	-0.2465	0.3886	0.0671	0.1326	0.2977	0.0132	0.2225	122.777	41.621	59.156
2	2.0573	-0.4107	0.1049	3.5292	-0.8473	3.7318	0.0554	-0.0873	0.3916	-0.1041	-0.0572	0.5472	-0.9094	-0.7014	0.0018	0.3923	0.2223	0.012	0.1944	-0.0825	0.2532	117.525	59.914	37.57
3	8.1429	-0.0879	-1.9158	10.08	-1.5531	6.2808	-0.0552	-0.4049	-0.0929	0.3717	-0.0576	0.4191	0.3651	-0.7088	0.1129	0.277	-0.0612	0.0245	0.2132	-0.0938	0.0948	117.503	36.231	35.209
4	4.0035	-2.0441	5.3231	3.6933	0.3132	12.4214	0.1648	-0.0332	-0.3815	-0.4393	-0.3843	1.0281	0.1085	-1.7423	0.2195	0.304	-0.0377	-0.1507	0.9347	0.0246	0.4159	108.261	55.134	24.282
5	1.9385	0.0643	-1.1919	5.4929	-0.7436	3.522	-0.093	0.1013	-0.0355	-0.0742	-0.0686	-0.2052	-0.1972	-0.1536	0.1616	0.2948	0.0128	0.0378	0.0909	-0.0522	0.1362	128.686	48.608	33.505
6	2.4995	-1.297	0.1144	4.1926	-1.1646	3.5191	-0.0311	-0.1773	0.3638	0.0595	0.0101	0.5095	-0.4057	-1.0107	0.0211	0.2617	0.1408	0.0436	0.3734	-0.1303	0.2542	112.283	52.125	44.089
7	11.9005	-7.2695	5.7963	13.8462	-5.6765	11.5669	-0.1974	-0.299	0.1046	0.0825	0.0194	-0.7715	0.3812	0.4917	0.1779	0.193	-0.005	0.0642	0.121	-0.0491	0.1072	132.746	46.08	48.277
8	8.8867	-6.4994	2.9197	10.297	-4.321	7.5832	0.1461	0.0487	0.8172	0.0259	-0.2951	-0.0089	-0.9791	-0.2962	0.149	0.3959	0.0869	0.0467	0.0702	-0.0614	0.1911	123.815	62.07	36.989
9	5.1335	0.2524	2.6879	13.6715	10.0611	12.005	-0.0721	0.8174	0.1697	-0.9723	0.035	-0.1485	-0.7899	0.3544	0.0372	0.3485	-0.0395	0.0229	0.1665	0.0753	0.0915	141.823	58.89	11.568
10	2.2111	1.538	-0.3806	4.647	-1.6208	3.1127	0.22	-0.1819	0.1769	0.3409	-0.2262	-0.451	-0.4311	0.1393	0.0063	0.4771	-0.0728	0.0054	0.0241	0.0041	0.2726	150.776	65.794	33.924
11	0.7269	0.1481	-0.015	10.0796	3.0264	2.8332	-0.0313	-0.0013	0.0518	-0.1714	-0.0804	0.0002	-0.0915	0.1012	0.1118	0.2908	-0.0123	-0.0045	0.0154	0.0067	0.1421	143.516	44.326	29.238
12	5.1164	-0.815	-1.9884	9.7337	3.9421	11.1632	-0.0127	0.0556	0.2177	-0.1474	0.3159	-0.6812	-0.139	0.6752	-0.3032	0.3001	0.0262	0.0713	0.0593	0.0265	0.2687	150.945	39.323	24.064
13	12.8362	5.2986	1.008	8.227	-5.1093	10.7435	-0.1349	-1.1012	-1.1145	0.3109	-0.6974	-1.4631	0.5348	0.9601	0.8322	0.3237	0.0908	-0.0815	0.2331	0.1452	0.314	155.53	54.065	41.819
14	1.0785	0.8214	0.213	3.5098	0.3804	1.562	-0.0508	0.1362	0.0122	-0.1904	0.0267	-0.4755	-0.1542	0.1187	0.024	0.3261	-0.0239	0.04	0.0275	0.0297	0.1992	148.675	54.68	23.178
15	6.7006	5.8876	7.901	10.5574	10.3085	16.4655	-0.0752	0.303	0.1556	-0.3742	-0.2439	0.9662	0.0596	-0.7779	0.3192	0.3449	0.0001	-0.0889	0.2038	-0.0337	0.3538	132.913	51.722	13.299
16	3.5105	2.8232	1.8875	6.173	1.9653	7.2068	0.1058	-0.1088	0.4414	0.1909	-0.1901	0.0135	-0.5088	0.0771	0.0842	0.396	-0.0275	0.019	0.0217	0.0316	0.2162	141.208	63.269	30.611

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-3 - 5
2	X-RAY DIFFRACTION	2	A	6 - 54
3	X-RAY DIFFRACTION	3	A	55 - 78
4	X-RAY DIFFRACTION	4	A	79 - 102
5	X-RAY DIFFRACTION	5	A	103 - 128
6	X-RAY DIFFRACTION	6	A	129 - 189
7	X-RAY DIFFRACTION	7	A	190 - 201
8	X-RAY DIFFRACTION	8	A	202 - 217
9	X-RAY DIFFRACTION	9	D	0 - 15
10	X-RAY DIFFRACTION	10	D	16 - 45
11	X-RAY DIFFRACTION	11	D	46 - 62
12	X-RAY DIFFRACTION	12	D	63 - 80
13	X-RAY DIFFRACTION	13	D	83 - 104
14	X-RAY DIFFRACTION	14	D	105 - 187
15	X-RAY DIFFRACTION	15	D	188 - 201
16	X-RAY DIFFRACTION	16	D	202 - 217

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