PDB-3guq: Crystal structure of novel carcinogenic factor of H. pylori

ID or keywords:

Entry

Database: PDB / ID: 3guq

Title

Crystal structure of novel carcinogenic factor of H. pylori

Components

Putative uncharacterized protein

Keywords

TOXIN / TNFa inducing factor / long alpha helix / Novel carcinogenic factor

Function / homology

Helicobacter TNF-alpha-Inducing protein / Helicobacter TNF-alpha-inducing protein / TNF-alpha-Inducing protein of Helicobacter / Thiol Ester Dehydrase; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / Tumor necrosis factor alpha-inducing protein

Function and homology information

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.47 Å

Authors

Tsurumura, T. / Tsuge, H. / Utsunomiya, H. / Kise, D. / Kuzuhara, T. / Fujiki, H. / Suganuma, M.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural basis for the Helicobacter pylori-carcinogenic TNF-alpha-inducing protein.
Authors: Tsuge, H. / Tsurumura, T. / Utsunomiya, H. / Kise, D. / Kuzuhara, T. / Watanabe, T. / Fujiki, H. / Suganuma, M.

History

Deposition	Mar 30, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3guq.cif.gz	43 KB	Display	PDBx/mmCIF format
PDB format	pdb3guq.ent.gz	31 KB	Display	PDB format
PDBx/mmJSON format	3guq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3guq_validation.pdf.gz	422.7 KB	Display	wwPDB validaton report
Full document	3guq_full_validation.pdf.gz	427.6 KB	Display
Data in XML	3guq_validation.xml.gz	9.3 KB	Display
Data in CIF	3guq_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/3guq ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guq	HTTPS FTP

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Related structure data

Similar structure data	2wcr-d 3gio-d 5y6o-3 6ipk-d 7abb-d 6fsh-3 4a5p-2 5y6o-1 5vvh-1 1lg9-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Putative uncharacterized protein

19 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

defined by author&software
38.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.518, 69.518, 69.161
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Putative uncharacterized protein / Novel carcinogenic factor / TNF-a inducing factor Mass: 19046.838 Da / Num. of mol.: 1 / Fragment: residues 1-166 (UNP residues 21-192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0596, HP_0596 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O25318
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	STRUCTURE WAS DETERMINED DELTIPA, WHICH IS N-TERMINAL DELETION MUTANT(2-LQACTC-7).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.44 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 6000, 5% MPD, 0.1M HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.47→50 Å / Num. all: 7160 / Num. obs: 7038 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 7 % / B_iso Wilson estimate: 70.382 Å² / R_sym value: 0.061 / Net I/σ(I): 21.3
Reflection shell	Resolution: 2.47→2.6 Å / Redundancy: 7.3 % / Num. unique all: 1006 / R_sym value: 0.133 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
REFMAC	5.1.24	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MIR / Resolution: 2.47→45.64 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.901 / SU B: 8.67 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2809	322	4.5 %	RANDOM
R_work	0.22641	-	-	-
obs	0.22897	6779	98.12 %	-

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: 39.455 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.28 Å²	1.14 Å²	0 Å²
2-	-	2.28 Å²	0 Å²
3-	-	-	-3.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.47→45.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1145	0	0	34	1179

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	1161
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1071
X-RAY DIFFRACTION	r_angle_refined_deg	1.844	1.951	1563
X-RAY DIFFRACTION	r_angle_other_deg	0.986	3	2504
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.353	5	141
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	179
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1265
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	217
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	302
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	1270
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.095	0.2	738
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.222	0.2	29
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	0.253	0.2	15
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.237	0.2	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.319	0.2	9
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	0.725	1.5	706
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.342	2	1149
X-RAY DIFFRACTION	r_scbond_it	2.196	3	455
X-RAY DIFFRACTION	r_scangle_it	3.653	4.5	414
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.47→2.534 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.264	24
R_work	0.211	494

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	12.2185	3.7666	2.5042	14.5284	1.7388	7.9021	-0.2848	-0.7915	1.164	0.5892	0.1093	0.8007	0.0765	-1.0778	0.1755	0.2925	-0.0221	0.1428	0.3535	-0.0885	0.2717	5.8024	12.6038	5.4645
2	4.0879	-3.8703	-4.9816	8.7282	9.7507	9.6626	-0.2818	0.3209	-0.2272	0.5818	-0.2035	-0.1279	0.9023	-0.3944	0.4853	0.4565	-0.0027	0.1979	0.1936	0.0972	0.1911	20.5035	4.9958	2.5014
3	5.2923	-10.5852	-2.9478	45.976	17.4114	9.4344	0.0931	-0.1429	-0.0483	-0.119	0.4714	-2.0739	-0.2043	0.1861	-0.5644	0.4111	0.0153	0.0908	0.0777	0.0379	0.2821	23.311	6.4571	5.4948
4	3.8474	2.5225	-10.385	20.3855	4.4927	2.7652	-0.4547	0.2021	-0.0126	-0.5095	0.1785	0.1315	0.1685	-0.4677	0.2762	0.2709	0.0019	-0.0373	0.2686	-0.0079	0.2397	19.79	21.5117	5.5849
5	5.1686	-6.2851	0.1375	5.2367	0.2065	4.7167	-0.1565	-0.279	0.7699	0.181	0.3004	0.0583	-0.2259	0.1919	-0.1439	0.2438	0.01	0.0131	0.26	-0.091	0.2684	21.1396	38.1169	6.7444
6	1.3326	2.0637	-2.3089	8.4464	-3.9102	6.0386	0.0007	-0.0888	-0.0829	0.1487	-0.0698	-0.6374	0.3676	0.5931	0.0691	0.2165	0.091	-0.0592	0.3014	-0.0281	0.2534	26.032	22.0483	8.3693
7	15.5029	-2.1477	6.0942	16.3899	12.2508	38.4458	1.1716	1.104	-1.8063	0.32	-0.3749	0.2556	1.8057	0.0476	-0.7967	0.3105	0.0477	0.0692	0.0371	-0.0551	0.4165	12.6187	1.5677	0.5098
8	12.6437	5.1159	8.4488	11.8192	7.6955	16.7056	0.3491	-0.6361	-0.5029	0.3183	-0.6769	0.1734	0.478	-0.6928	0.3278	0.3657	-0.043	0.1148	0.1502	0.027	0.1555	14.9292	8.6297	5.9566
9	9.7551	5.8697	-6.4732	11.0878	-1.316	6.8459	0.6237	-0.5802	0.1173	1.0867	-0.332	-0.7301	0.1773	0.6377	-0.2917	0.2256	0.0825	-0.1844	0.3372	-0.0269	0.2282	29.1077	25.2864	16.1597
10	3.7597	6.0409	-2.1354	11.3798	0.4626	3.1944	0.1057	-0.4137	0.4674	0.8916	-0.1202	0.1117	0.0715	0.1213	0.0146	0.2408	0.0553	-0.0603	0.3434	-0.0989	0.2403	22.3315	31.4829	15.4838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 31
2	X-RAY DIFFRACTION	2	A	32 - 48
3	X-RAY DIFFRACTION	3	A	49 - 59
4	X-RAY DIFFRACTION	4	A	60 - 68
5	X-RAY DIFFRACTION	5	A	69 - 84
6	X-RAY DIFFRACTION	6	A	85 - 106
7	X-RAY DIFFRACTION	7	A	107 - 116
8	X-RAY DIFFRACTION	8	A	117 - 123
9	X-RAY DIFFRACTION	9	A	124 - 140
10	X-RAY DIFFRACTION	10	A	141 - 160

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