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- PDB-5ovt: Thiobacillus denitrificans BPH in complex with Epoxomicin -

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Basic information

Entry
Database: PDB / ID: 5ovt
TitleThiobacillus denitrificans BPH in complex with Epoxomicin
Components
  • BPH
  • Epoxomicin
KeywordsHYDROLASE / Protein Degradation / beta-proteobacteria proteasome homologue / covalent proteasome inhibitor
Function / homologyNucleophile aminohydrolases, N-terminal / PHOSPHATE ION / BPH
Function and homology information
Biological speciesThiobacillus denitrificans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsFuchs, A.C.D. / Albrecht, R. / Martin, J. / Hartmann, M.D.
CitationJournal: 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
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 3.0Mar 6, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPH
B: BPH
C: BPH
D: BPH
E: BPH
F: BPH
G: BPH
a: Epoxomicin
b: Epoxomicin
c: Epoxomicin
d: Epoxomicin
e: Epoxomicin
f: Epoxomicin
g: Epoxomicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,92021
Polymers158,25514
Non-polymers6657
Water1,42379
1
A: BPH
B: BPH
C: BPH
D: BPH
E: BPH
F: BPH
G: BPH
a: Epoxomicin
b: Epoxomicin
c: Epoxomicin
d: Epoxomicin
e: Epoxomicin
f: Epoxomicin
g: Epoxomicin
hetero molecules

A: BPH
B: BPH
C: BPH
D: BPH
E: BPH
F: BPH
G: BPH
a: Epoxomicin
b: Epoxomicin
c: Epoxomicin
d: Epoxomicin
e: Epoxomicin
f: Epoxomicin
g: Epoxomicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,83942
Polymers316,51028
Non-polymers1,33014
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area67580 Å2
ΔGint-468 kcal/mol
Surface area79020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.820, 196.820, 296.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 190 / Label seq-ID: 1 - 190

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17BB
27CC
18BB
28DD
19BB
29EE
110BB
210FF
111BB
211GG
112CC
212DD
113CC
213EE
114CC
214FF
115CC
215GG
116DD
216EE
117DD
217FF
118DD
218GG
119EE
219FF
120EE
220GG
121FF
221GG

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

#1: Protein
BPH


Mass: 22065.072 Da / Num. of mol.: 7
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: Protein/peptide
Epoxomicin


Mass: 542.752 Da / Num. of mol.: 7 / Source method: obtained synthetically / Details: covalent proteasome inhibitor / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCBI Reference Sequence: WP_018076511.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.11 Å3/Da / Density % sol: 75.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 100 mM sodium acetate pH 4.8, 1.2 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→39.2 Å / Num. obs: 71632 / % possible obs: 99.9 % / Redundancy: 57.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.439 / Net I/σ(I): 13.6
Reflection shellResolution: 2.95→3.12 Å / Redundancy: 57.6 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 3.11 / Num. unique obs: 10916 / CC1/2: 0.878 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→39.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 17.559 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.22 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 3609 5 %RANDOM
Rwork0.17242 ---
obs0.17323 68023 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 2.95→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10073 0 35 79 10187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910416
X-RAY DIFFRACTIONr_bond_other_d0.0080.029877
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.97214084
X-RAY DIFFRACTIONr_angle_other_deg1.173322589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8922.903434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.661151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4031563
X-RAY DIFFRACTIONr_chiral_restr0.1070.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111620
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7382.6635236
X-RAY DIFFRACTIONr_mcbond_other2.7382.6625235
X-RAY DIFFRACTIONr_mcangle_it3.8713.9186482
X-RAY DIFFRACTIONr_mcangle_other3.8713.9196483
X-RAY DIFFRACTIONr_scbond_it4.2143.1585179
X-RAY DIFFRACTIONr_scbond_other4.0733.1325152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4144.567561
X-RAY DIFFRACTIONr_long_range_B_refined7.53821.91911180
X-RAY DIFFRACTIONr_long_range_B_other7.53921.92311181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111250.01
12B111250.01
21A110840.03
22C110840.03
31A111230.01
32D111230.01
41A110800.02
42E110800.02
51A111230.01
52F111230.01
61A110750.03
62G110750.03
71B110940.03
72C110940.03
81B111270.01
82D111270.01
91B110910.02
92E110910.02
101B111290.01
102F111290.01
111B110820.03
112G110820.03
121C110880.03
122D110880.03
131C110730.03
132E110730.03
141C110840.03
142F110840.03
151C110980.02
152G110980.02
161D110900.02
162E110900.02
171D111230.01
172F111230.01
181D110780.03
182G110780.03
191E110810.02
192F110810.02
201E110510.03
202G110510.03
211F110720.03
212G110720.03
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 258 -
Rwork0.316 4945 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.68130.28080.16110.6461-0.18330.4802-0.02170.1496-0.21280.01250.0216-0.0740.01580.03940.00010.0462-0.02720.06670.1744-0.14820.1874-16.861569.2212-1.4342
20.78090.0469-0.17650.2634-0.10130.6348-0.02650.0877-0.15610.0308-0.05840.02980.074-0.00660.08490.0927-0.06950.03870.0855-0.09620.217-43.023261.893614.0591
30.5729-0.10320.07580.3753-0.04490.72690.0465-0.0058-0.08860.1027-0.09340.04960.04750.0080.0470.1405-0.10570.06710.1038-0.00780.1619-51.955671.133642.6291
40.80730.00170.23330.6310.27560.26570.0853-0.1341-0.08410.1622-0.09870.050.05170.02770.01340.1875-0.13270.04780.1970.0150.0427-37.236789.818762.9272
50.70920.0343-0.10010.75890.03050.19170.0888-0.147-0.03930.106-0.07-0.01340.00030.1142-0.01880.1529-0.1101-0.03030.2349-0.02150.0224-9.627103.997759.3807
60.2802-0.0606-0.340.67050.01880.7570.0418-0.0248-0.07030.0888-0.0407-0.0702-0.04150.1586-0.00110.0345-0.0477-0.03820.2411-0.04340.12829.9759103.026235.0279
70.38410.1479-0.02740.7356-0.02190.5409-0.02990.0692-0.1280.02940.0169-0.094-0.01180.05190.0130.0192-0.01410.04640.2361-0.08750.16476.649187.61198.0158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 190
2X-RAY DIFFRACTION2B1 - 190
3X-RAY DIFFRACTION3C1 - 190
4X-RAY DIFFRACTION4D1 - 190
5X-RAY DIFFRACTION5E1 - 190
6X-RAY DIFFRACTION6F1 - 190
7X-RAY DIFFRACTION7G1 - 190

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