PDB-3tja: Crystal structure of Helicobacter pylori UreE in the apo form

ID or keywords:

Entry

Database: PDB / ID: 3tja

Title

Crystal structure of Helicobacter pylori UreE in the apo form

Components

Urease accessory protein ureE

Keywords

METAL BINDING PROTEIN

Function / homology

Function and homology information

urea metabolic process / nickel cation binding / unfolded protein binding / protein folding / protein-containing complex assembly / cytoplasm
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Banaszak, K. / Bellucci, M. / Zambelli, B. / Rypniewski, W.R. / Ciurli, S.

Citation

Journal: Biochem.J. / Year: 2012
Title: Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking.
Authors: Banaszak, K. / Martin-Diaconescu, V. / Bellucci, M. / Zambelli, B. / Rypniewski, W. / Maroney, M.J. / Ciurli, S.

History

Deposition	Aug 24, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3tja.cif.gz	251.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3tja.ent.gz	204.8 KB	Display	PDB format
PDBx/mmJSON format	3tja.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tja_validation.pdf.gz	468.5 KB	Display	wwPDB validaton report
Full document	3tja_full_validation.pdf.gz	479.4 KB	Display
Data in XML	3tja_validation.xml.gz	24.2 KB	Display
Data in CIF	3tja_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/3tja ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tja	HTTPS FTP

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Related structure data

Related structure data	3tj8SC 3tj9C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3la0-1 3l9z-1 1ear-1 3la0-2 3tj9-1 1gmv-d 1eb0-1 1zxt-d 5ag9-d 5ag8-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Urease accessory protein ureE

B: Urease accessory protein ureE

C: Urease accessory protein ureE

D: Urease accessory protein ureE

hetero molecules

78.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Urease accessory protein ureE

B: Urease accessory protein ureE

hetero molecules

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

2

C: Urease accessory protein ureE

D: Urease accessory protein ureE

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.999, 70.468, 123.340
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Urease accessory protein ureE Mass: 19437.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureE, HP_0070 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09064
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	TYR 22 IS AGREES WITH THE SEQUENCE IN GB ABM16833.1

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 23, 2010
Radiation	Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 41018 / % possible obs: 99.7 % / Redundancy: 5.5 % / R_sym value: 0.06 / Net I/σ(I): 21.6
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1957 / R_sym value: 0.593 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TJ8

3tj8

Resolution: 2→19.701 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.94 / SU B: 11.476 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26695	2045	5 %	RANDOM
R_work	0.20767	-	-	-
obs	0.21066	38745	98.53 %	-

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: 43.556 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.75 Å²	0 Å²	0 Å²
2-	-	-1.45 Å²	0 Å²
3-	-	-	-1.3 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.701 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4723	0	21	100	4844

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	4826
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.947	1.984	6515
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.91	5	597
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.729	24.346	214
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.643	15	906
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.03	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	755
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	3526
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	1.135	1.5	2978
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.93	2	4793
X-RAY DIFFRACTION	r_scbond_it	3.307	3	1848
X-RAY DIFFRACTION	r_scangle_it	5.262	4.5	1719
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	136	-
R_work	0.248	2538	-
obs	-	-	88.81 %

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	4.6829	3.7668	-2.6779	3.1315	-1.6347	4.7551	-0.1687	-0.0659	-0.0286	-0.0304	-0.032	0.0734	0.5285	0.014	0.2007	0.1671	0.0289	0.0698	0.1717	0.1308	0.2679	-15.399	-0.4999	3.9104
2	3.5896	-1.2533	-0.4992	4.7222	-0.0304	2.4924	-0.0028	-0.168	-0.246	0.0991	0.0444	0.018	0.3041	0.077	-0.0416	0.0598	-0.0111	-0.0171	0.1028	0.047	0.1085	-11.3214	5.9967	-0.3723
3	2.1828	1.4056	1.6285	3.4598	1.5194	2.3291	-0.0122	0.223	0.0256	-0.0957	-0.0919	-0.0459	-0.1401	0.0547	0.1042	0.1007	0.0053	-0.0572	0.0729	0	0.0692	-27.9465	13.7959	-23.1234
4	3.1118	-0.5721	1.107	6.6743	0.4202	3.1702	0.0647	0.012	0.1824	0.0727	-0.229	-0.0721	-0.108	-0.1738	0.1643	0.1144	-0.0025	-0.0747	0.0868	-0.02	0.072	-26.8291	16.6769	-20.4277
5	3.6785	2.1902	2.7614	4.7399	-0.6211	7.5623	0.2703	-0.0879	-0.4415	0.2478	-0.2272	-0.1652	0.5743	-0.1213	-0.0432	0.1117	-0.0185	-0.0447	0.1401	0.0322	0.1744	-22.8813	11.5375	-13.1194
6	2.071	-1.3479	-0.8103	2.4908	-0.1189	2.9218	0.1356	-0.025	0.2924	0.0152	-0.0433	-0.0178	-0.008	-0.1771	-0.0923	0.1686	-0.0285	-0.0095	0.1858	-0.0618	0.1589	-43.6353	11.2655	-52.3774
7	3.8161	-1.1507	-2.0297	4.1126	-0.2101	5.6584	0.3008	0.1796	0.4818	-0.0757	-0.0265	-0.2691	-0.2743	-0.1474	-0.2743	0.1019	-0.0138	-0.0067	0.1266	-0.0292	0.1375	-39.7428	11.1516	-55.1141
8	0.3547	0.8264	0.6336	5.3764	2.2207	5.9875	0.0159	-0.0923	-0.0491	0.1172	-0.1511	0.102	0.3072	-0.3606	0.1352	0.1045	-0.0341	-0.0458	0.1072	-0.0161	0.0874	-34.8516	1.7269	-29.3559
9	16.9073	-0.7325	-8.2971	4.2054	3.3452	17.2861	-0.1256	-0.3438	-0.8473	0.8316	-0.1624	-0.7552	1.2701	0.615	0.288	0.3656	0.014	-0.1416	0.126	0.0364	0.2751	-30.486	-7.1811	-28.5218
10	2.7239	-1.4403	3.9148	18.0799	3.27	8.0117	-0.2678	0.0638	0.1162	-0.265	0.1126	0.0532	-0.7774	-0.1176	0.1552	0.1926	0.0384	-0.0078	0.1634	-0.0166	0.0563	-36.9155	4.4652	-37.7809
11	3.6978	0.3257	1.7427	1.6732	0.6494	2.2617	-0.1689	0.0699	0.1977	-0.423	-0.0585	0.1823	-0.1056	0.0015	0.2274	0.1364	-0.0136	-0.0126	0.1391	0.0359	0.1465	-13.7004	32.3997	-11.6439
12	3.3306	1.2486	-0.2943	3.054	-0.0849	2.1236	0.0311	-0.1371	0.221	0.0317	-0.019	-0.1072	-0.2393	0.1439	-0.0121	0.0343	-0.0141	-0.0093	0.1189	0.0104	0.0984	-9.6495	29.8329	-2.7287
13	2.4461	-0.8437	-1.2989	2.8563	-0.077	2.4173	-0.0473	-0.074	0.0624	0.0195	-0.0582	-0.0239	0.0139	0.1016	0.1055	0.075	-0.0224	0.0013	0.1224	0.002	0.0537	-28.623	22.6664	15.0328
14	22.7011	-0.7136	-0.4733	6.2477	0.9362	7.2112	-0.2801	-0.8613	-0.5013	0.8315	0.1667	-0.1839	0.1788	0.0877	0.1134	0.1788	0.0461	0.0356	0.1243	0.0708	0.0956	-25.7963	14.4705	20.1692
15	4.7118	-3.8071	-3.9364	12.8517	1.533	5.855	0.2735	-0.1587	0.3975	-0.0053	-0.0352	-0.1495	-0.3716	0.2101	-0.2383	0.0263	-0.0213	0.0244	0.1675	0.0526	0.155	-22.2102	24.4648	7.2614
16	3.1271	0.1346	0.4159	4.0178	-0.1228	4.1739	-0.0306	0.1385	-0.2233	-0.0645	-0.0667	0.3986	0.0266	-0.2731	0.0974	0.1042	0.0253	0.0198	0.152	-0.0808	0.16	-41.9317	23.6948	46.9325
17	16.9289	-14.1254	-3.5392	16.2818	3.1602	4.9081	-0.0621	-0.0296	-0.5416	0.4125	-0.1723	0.5418	0.1807	0.0108	0.2344	0.087	-0.0436	0.0127	0.1242	-0.0312	0.1416	-39.4319	25.54	53.9336
18	3.5144	1.8658	-0.6582	8.9073	-1.1107	4.9034	0.1903	-0.1277	-0.089	-0.0301	-0.043	0.4227	-0.1041	-0.3861	-0.1472	0.0545	0.0166	-0.0101	0.1871	-0.0746	0.0906	-43.486	24.1982	45.8992
19	0.2466	-1.0417	-0.4088	6.0555	1.0754	6.3996	0.0295	0.0148	0.1742	0.1249	0.1627	-0.3818	-0.8514	0.1062	-0.1922	0.2381	-0.0358	0.0417	0.1692	0.0209	0.2262	-33.1808	36.1475	23.6463
20	1.4657	1.6993	-1.6453	12.9279	-1.6242	8.4468	-0.3343	0.2723	0.0486	0.321	0.3693	-0.378	0.0562	-0.0485	-0.035	0.1909	-0.0206	-0.037	0.1967	-0.0298	0.0881	-37.2271	30.9649	32.248

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 14
2	X-RAY DIFFRACTION	2	A	15 - 77
3	X-RAY DIFFRACTION	3	A	78 - 104
4	X-RAY DIFFRACTION	4	A	105 - 133
5	X-RAY DIFFRACTION	5	A	134 - 149
6	X-RAY DIFFRACTION	6	B	1 - 30
7	X-RAY DIFFRACTION	7	B	31 - 77
8	X-RAY DIFFRACTION	8	B	78 - 118
9	X-RAY DIFFRACTION	9	B	119 - 133
10	X-RAY DIFFRACTION	10	B	134 - 150
11	X-RAY DIFFRACTION	11	C	1 - 23
12	X-RAY DIFFRACTION	12	C	24 - 78
13	X-RAY DIFFRACTION	13	C	79 - 118
14	X-RAY DIFFRACTION	14	C	119 - 133
15	X-RAY DIFFRACTION	15	C	134 - 148
16	X-RAY DIFFRACTION	16	D	1 - 36
17	X-RAY DIFFRACTION	17	D	37 - 51
18	X-RAY DIFFRACTION	18	D	52 - 79
19	X-RAY DIFFRACTION	19	D	80 - 133
20	X-RAY DIFFRACTION	20	D	134 - 150

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