PDB-5ovs: Thiobacillus denitrificans BPH

ID or keywords:

Entry

Database: PDB / ID: 5ovs

Title

Thiobacillus denitrificans BPH

Components

BPH

Keywords

HYDROLASE /

Protein Degradation / beta-proteobacteria proteasome homologue

Function / homology

Nucleophile aminohydrolases, N-terminal / BPH

Function and homology information

Biological species

Thiobacillus denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Fuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D.

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.
Authors: Fuchs, A.C.D. / Maldoner, L. / Hipp, K. / Hartmann, M.D. / Martin, J.

History

Deposition	Aug 29, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 31, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ovs.cif.gz	950.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ovs.ent.gz	823.3 KB	Display	PDB format
PDBx/mmJSON format	5ovs.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/ov/5ovs ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovs	HTTPS FTP

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Related structure data

Related structure data	5ovtC 5ovuC C: citing same article (ref.)
Similar structure data	5ovt-1 5y9n-1 5y9n-2 2ayt-3 2dzy-1 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	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: BPH

B: BPH

C: BPH

D: BPH

E: BPH

F: BPH

G: BPH

H: BPH

I: BPH

J: BPH

K: BPH

L: BPH

M: BPH

N: BPH

306 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	79.107, 175.230, 205.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L
13	1	M
14	1	N

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	1 - 999
2	1	1	5	B	1 - 999
3	1	1	5	C	1 - 999
4	1	1	5	D	1 - 999
5	1	1	5	E	1 - 999
6	1	1	5	F	1 - 999
7	1	1	5	G	1 - 999
8	1	1	5	H	1 - 999
9	1	1	5	I	1 - 999
10	1	1	5	J	1 - 999
11	1	1	5	K	1 - 999
12	1	1	5	L	1 - 999
13	1	1	5	M	1 - 999
14	1	1	5	N	1 - 999

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.966831, -0.048489, 0.250772), (-0.157226, 0.66077, 0.733937), (-0.201291, -0.749021, 0.631229)	-7.44026, -23.47234, 5.96701
3	given	(0.890535, -0.278575, 0.359643), (-0.40261, -0.114585, 0.908172), (-0.211785, -0.953554, -0.214199)	-12.21901, -33.65191, 28.76868
4	given	(0.823842, -0.511659, 0.243906), (-0.566674, -0.733712, 0.374897), (-0.012863, -0.44707, -0.894406)	-10.46084, -22.98518, 51.92661
5	given	(0.823173, -0.567674, -0.011472), (-0.511957, -0.73334, -0.44734), (0.24553, 0.374111, -0.894291)	-3.44606, 1.13619, 57.8182
6	given	(0.882731, -0.417199, -0.216171), (-0.286217, -0.11256, -0.95153), (0.372646, 0.901818, -0.21877)	3.66788, 19.91925, 41.95966
7	given	(0.963298, -0.161412, -0.214483), (-0.056936, 0.657976, -0.750883), (0.262327, 0.735536, 0.624637)	5.38118, 19.43062, 16.16075
8	given	(-0.892212, 0.267923, -0.363558), (0.275761, -0.314319, -0.908383), (-0.35765, -0.910726, 0.206556)	-27.27483, 29.99743, 14.33257
9	given	(-0.966781, 0.049308, -0.250805), (0.05129, -0.923836, -0.379336), (-0.250407, -0.379598, 0.890619)	-31.80186, 10.16452, -2.2179
10	given	(-0.999971, 0.005048, 0.005638), (-0.002003, -0.894977, 0.446108), (0.007298, 0.446084, 0.894961)	-39.68605, -13.74912, 3.44158
11	given	(-0.962235, 0.161198, 0.21936), (0.171836, -0.265302, 0.948729), (0.21113, 0.950595, 0.227583)	-44.67605, -23.85714, 26.44023
12	given	(-0.883664, 0.41371, 0.219047), (0.422358, 0.502819, 0.754179), (0.20187, 0.758958, -0.619057)	-42.93815, -12.89692, 49.55977
13	given	(-0.825642, 0.564162, 0.006072), (0.564195, 0.825588, 0.009462), (0.000326, 0.011238, -0.999937)	-35.86105, 11.10244, 55.48794
14	given	(-0.830275, 0.49661, -0.253025), (0.498277, 0.457967, -0.736197), (-0.249725, -0.737322, -0.627689)	-28.99772, 29.96328, 39.47754

#1: Protein	BPH Mass: 21877.494 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thiobacillus denitrificans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFN0*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	NCBI Reference Sequence: WP_018076511.1

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.46 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES-NaOH pH 7.0, 600 mM NaF

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→39.6 Å / Num. obs: 127579 / % possible obs: 99.7 % / Redundancy: 5.22 % / CC_1/2: 0.997 / R_merge(I) obs: 0.113 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.3→2.44 Å / Redundancy: 5.14 % / R_merge(I) obs: 0.831 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 20143 / CC_1/2: 0.704 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
XDS		data reduction
XDS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→39.55 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.916 / SU B: 21.664 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25523	6379	5 %	RANDOM
R_work	0.20798	-	-	-
obs	0.21034	121199	99.72 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 42.195 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.94 Å²	0 Å²	-0 Å²
2-	-	0.1 Å²	-0 Å²
3-	-	-	-3.04 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→39.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19861	0	0	493	20354

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	20310
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	18987
X-RAY DIFFRACTION	r_angle_refined_deg	1.188	1.95	27572
X-RAY DIFFRACTION	r_angle_other_deg	0.735	3	43552
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.937	5	2565
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.178	23.19	884
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.724	15	3125
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.833	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	3070
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	23119
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4735
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	1.185	2.946	10344
X-RAY DIFFRACTION	r_mcbond_other	1.185	2.945	10343
X-RAY DIFFRACTION	r_mcangle_it	2.033	4.408	12881
X-RAY DIFFRACTION	r_mcangle_other	2.032	4.408	12882
X-RAY DIFFRACTION	r_scbond_it	1.228	3.135	9966
X-RAY DIFFRACTION	r_scbond_other	1.228	3.136	9967
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.095	4.652	14692
X-RAY DIFFRACTION	r_long_range_B_refined	3.931	23.775	22840
X-RAY DIFFRACTION	r_long_range_B_other	3.915	23.738	22769
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 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	1088	medium positional	0.15	0.5
B	1088	medium positional	0.16	0.5
C	1088	medium positional	0.18	0.5
D	1088	medium positional	0.15	0.5
E	1088	medium positional	0.16	0.5
F	1088	medium positional	0.18	0.5
G	1088	medium positional	0.17	0.5
H	1088	medium positional	0.24	0.5
J	1088	medium positional	0.16	0.5
J	1088	medium positional	0.16	0.5
K	1088	medium positional	0.17	0.5
L	1088	medium positional	0.15	0.5
M	1088	medium positional	0.14	0.5
N	1088	medium positional	0.16	0.5
A	1684	loose positional	0.34	5
B	1684	loose positional	0.32	5
C	1684	loose positional	0.33	5
D	1684	loose positional	0.42	5
E	1684	loose positional	0.48	5
F	1684	loose positional	0.33	5
G	1684	loose positional	0.37	5
H	1684	loose positional	0.38	5
I	1684	loose positional	0.43	5
J	1684	loose positional	0.41	5
K	1684	loose positional	0.43	5
L	1684	loose positional	0.44	5
M	1684	loose positional	0.4	5
N	1684	loose positional	0.28	5
A	1088	medium thermal	2.27	2
B	1088	medium thermal	7.17	2
C	1088	medium thermal	4.93	2
D	1088	medium thermal	3.46	2
E	1088	medium thermal	6.54	2
F	1088	medium thermal	3.61	2
G	1088	medium thermal	2.69	2
H	1088	medium thermal	5.28	2
I	1088	medium thermal	4.29	2
J	1088	medium thermal	4.55	2
K	1088	medium thermal	6.36	2
L	1088	medium thermal	3.69	2
M	1088	medium thermal	5.69	2
N	1088	medium thermal	7.72	2
A	1684	loose thermal	2.53	10
B	1684	loose thermal	7.28	10
C	1684	loose thermal	5.35	10
D	1684	loose thermal	3.68	10
E	1684	loose thermal	7.01	10
F	1684	loose thermal	4.37	10
G	1684	loose thermal	3.17	10
H	1684	loose thermal	5.5	10
I	1684	loose thermal	4.55	10
J	1684	loose thermal	4.98	10
K	1684	loose thermal	6.34	10
L	1684	loose thermal	4.17	10
M	1684	loose thermal	5.79	10
N	1684	loose thermal	7.77	10

LS refinement shell

Resolution: 2.299→2.358 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.391	453	-
R_work	0.346	8604	-
obs	-	-	97.18 %

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	0.4538	-0.2129	0.4831	0.5692	0.0618	0.7029	-0.0214	0.037	-0.0458	0.107	-0.0072	0.1475	0.0211	-0.0099	0.0287	0.0349	-0.0382	0.0625	0.2075	0.0155	0.2009	-43.4576	-13.6784	56.5573
2	0.2417	-0.3223	-0.1063	0.5169	-0.1459	1.1284	-0.0525	0.0461	-0.0555	0.0626	0.0089	0.1109	0.0951	-0.142	0.0436	0.0481	-0.0738	-0.0089	0.1764	-0.0383	0.2321	-46.5507	-29.6887	30.086
3	0.4273	0.1312	-0.5451	0.7719	-0.3128	0.7409	-0.0589	0.0385	0.0103	-0.1019	0.1025	0.1309	0.1147	-0.1168	-0.0436	0.0762	-0.0663	-0.0653	0.2197	-0.0722	0.1704	-41.751	-20.0882	0.9574
4	0.4516	0.1341	-0.3375	0.9333	0.0369	0.2823	-0.0164	0.0652	0.0229	-0.0857	0.0293	0.124	0.0185	-0.0748	-0.0129	0.0462	-0.0148	-0.0632	0.2488	-0.0378	0.1006	-32.5149	7.9731	-8.7172
5	0.4602	0.1408	-0.1315	0.422	0.2319	0.4676	-0.0009	0.0683	-0.0109	0.0071	-0.0073	0.0276	-0.053	-0.0681	0.0082	0.0713	0.0209	-0.0092	0.1731	0.0219	0.1246	-25.6432	33.1165	8.1948
6	0.573	0.1062	0.033	0.146	-0.3195	0.8652	-0.006	0.0472	-0.0352	0.078	0.0425	0.0182	-0.2103	-0.1248	-0.0365	0.1191	0.0269	0.0087	0.131	0.019	0.114	-26.5338	36.6285	38.9569
7	0.4679	0.1142	0.0471	0.7404	-0.1426	0.4746	-0.0363	-0.0283	-0.0685	0.0769	0.0283	0.0754	-0.1523	-0.0839	0.0081	0.065	0.0143	0.0348	0.2098	0.0308	0.1059	-34.5468	15.8251	60.5697
8	0.2978	0.2075	-0.0333	0.5955	0.2224	0.8269	-0.0246	-0.0525	-0.0311	0.013	-0.0208	0.0138	0.1547	0.0977	0.0454	0.0716	0.0044	-0.0049	0.1318	0.0617	0.1465	-12.7065	-29.0785	54.2835
9	0.2918	0.074	-0.4007	0.7834	0.216	0.7129	0.002	-0.0257	0.0133	0.0781	0.0002	-0.064	0.0545	0.0622	-0.0022	0.0521	-0.0254	-0.0112	0.1977	0.0752	0.1035	-4.6699	-0.87	64.3157
10	0.4193	-0.3415	-0.2338	0.4575	-0.1222	0.697	-0.062	0.009	-0.0223	0.1205	-0.0648	-0.07	-0.0728	0.0662	0.1268	0.0798	-0.0829	-0.0563	0.1762	0.0594	0.1113	4.2373	23.6742	47.5271
11	0.175	-0.3259	-0.0967	0.6739	0.0613	0.8936	0.008	0.0188	-0.0103	0.0395	-0.0873	-0.0585	-0.0796	0.0775	0.0793	0.0658	-0.0547	-0.0266	0.1725	0.0589	0.1214	7.0705	26.1574	16.6166
12	0.3163	0.0048	0.2869	1.1	-0.086	0.6312	-0.0111	0.0468	-0.0212	-0.0572	-0.0257	-0.1164	0.0138	0.0448	0.0368	0.0459	0.0097	0.0296	0.1823	-0.0022	0.1207	1.5451	4.7146	-5.0442
13	0.4129	0.2327	0.1876	0.7469	-0.3174	0.5854	-0.0735	0.0444	-0.0005	-0.0902	-0.0241	-0.0883	0.1421	0.0327	0.0976	0.1868	0.0213	0.0144	0.0993	-0.0576	0.0658	-7.7169	-24.7237	-1.3624
14	0.8152	0.276	0.1644	0.1584	-0.1594	0.8599	-0.0772	-0.0416	-0.0686	-0.0938	-0.0413	-0.0302	0.1383	0.0641	0.1185	0.1921	0.0159	-0.007	0.0262	-0.0276	0.1419	-14.0105	-39.7675	25.0605

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 190
2	X-RAY DIFFRACTION	2	B	1 - 190
3	X-RAY DIFFRACTION	3	C	1 - 190
4	X-RAY DIFFRACTION	4	D	1 - 190
5	X-RAY DIFFRACTION	5	E	1 - 190
6	X-RAY DIFFRACTION	6	F	1 - 190
7	X-RAY DIFFRACTION	7	G	1 - 190
8	X-RAY DIFFRACTION	8	H	1 - 190
9	X-RAY DIFFRACTION	9	I	1 - 190
10	X-RAY DIFFRACTION	10	J	1 - 191
11	X-RAY DIFFRACTION	11	K	1 - 192
12	X-RAY DIFFRACTION	12	L	1 - 190
13	X-RAY DIFFRACTION	13	M	1 - 190
14	X-RAY DIFFRACTION	14	N	1 - 190

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Yorodumi