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- PDB-5trs: Structure of Mycobacterium tuberculosis proteasome in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5trs
TitleStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2144
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE inhibitor / Mycobacterium tuberculosis / proteasome / N / C-capped dipeptide / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-tert-butoxy-N~2~-(5-methyl-1,2-oxazole-3-carbonyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide / Chem-7HZ / Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.08356699278 Å
AuthorsHsu, H.-C. / Fan, H. / Singh, P.K. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070285 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.
Authors: Hsu, H.C. / Singh, P.K. / Fan, H. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.name
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit alpha
Q: Proteasome subunit alpha
R: Proteasome subunit alpha
S: Proteasome subunit alpha
T: Proteasome subunit alpha
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)725,19842
Polymers717,44728
Non-polymers7,75014
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84620 Å2
ΔGint-80 kcal/mol
Surface area219410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.509, 198.301, 165.941
Angle α, β, γ (deg.)90.000, 103.133, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
12
22
32
42
52
62
72
82
92
102
112
122
132
142

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 7
121(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N8
131(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
141(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
151(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
161(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
171(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
181(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
191(CHAIN N AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...N1 - 223
211(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 7
221(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H8
231(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
241(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
251(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
261(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
271(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
281(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
291(CHAIN H AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...H1 - 222
311(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 7
321(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I8
331(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
341(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
351(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
361(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
371(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
381(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
391(CHAIN I AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...I1 - 222
411(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 7
421(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J8
431(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
441(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
451(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
461(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
471(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
481(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
491(CHAIN J AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...J1 - 222
511(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 7
521(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K8
531(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
541(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
551(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
561(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
571(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
581(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
591(CHAIN K AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...K1 - 223
611(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 7
621(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L8
631(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
641(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
651(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
661(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
671(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
681(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
691(CHAIN L AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...L1 - 223
711(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 7
721(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M8
731(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
741(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
751(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
761(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
771(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
781(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
791(CHAIN M AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...M1 - 222
811(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 7
821(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V8
831(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
841(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
851(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
861(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
871(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
881(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
891(CHAIN V AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...V1 - 223
911(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 7
921(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W8
931(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
941(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
951(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
961(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
971(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
981(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
991(CHAIN W AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...W1 - 223
1011(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 7
1021(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X8
1031(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1041(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1051(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1061(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1071(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1081(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1091(CHAIN X AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...X1 - 222
1111(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 7
1121(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y8
1131(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1141(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1151(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1161(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1171(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1181(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1191(CHAIN Y AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Y1 - 223
1211(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 7
1221(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z8
1231(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1241(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1251(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1261(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1271(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1281(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1291(CHAIN Z AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...Z1 - 222
1311(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A1 - 7
1321(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A8
1331(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1341(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1351(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1361(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1371(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1381(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1391(CHAIN A AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...A9 - 235
1411(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B1 - 7
1421(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B8
1431(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1441(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1451(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1461(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1471(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1481(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
1491(CHAIN B AND (RESSEQ 1:7 OR (RESID 8 AND (NAME...B9 - 236
112(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A12 - 13
122(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A15 - 25
132(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A27 - 34
142(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A35
152(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
162(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
172(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
182(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
192(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
1102(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
1112(CHAIN A AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...A9 - 235
212(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B12 - 13
222(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B15 - 25
232(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B27 - 34
242(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B35
252(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
262(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
272(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
282(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
292(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
2102(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
2112(CHAIN B AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...B9 - 236
312(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C12 - 13
322(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C15 - 25
332(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C27 - 34
342(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C35
352(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
362(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
372(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
382(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
392(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
3102(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
3112(CHAIN C AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...C9 - 236
412(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D12 - 13
422(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D15 - 25
432(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D27 - 34
442(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D35
452(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
462(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
472(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
482(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
492(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
4102(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
4112(CHAIN D AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...D9 - 235
512(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E12 - 13
522(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E15 - 25
532(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E27 - 34
542(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E35
552(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
562(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
572(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
582(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
592(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
5102(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
5112(CHAIN E AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...E9 - 235
612(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F12 - 13
622(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F15 - 25
632(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F27 - 34
642(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F35
652(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
662(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
672(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
682(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
692(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
6102(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
6112(CHAIN F AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...F9 - 234
712(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G12 - 13
722(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G15 - 25
732(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G27 - 34
742(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G35
752(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
762(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
772(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
782(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
792(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
7102(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
7112(CHAIN G AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...G9 - 235
812(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O12 - 13
822(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O15 - 25
832(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O27 - 34
842(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O35
852(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
862(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
872(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
882(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
892(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
8102(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
8112(CHAIN O AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...O9 - 235
912(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P12 - 13
922(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P15 - 25
932(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P27 - 34
942(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P35
952(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
962(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
972(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
982(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
992(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
9102(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
9112(CHAIN P AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...P9 - 236
1012(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q12 - 13
1022(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q15 - 25
1032(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q27 - 34
1042(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q35
1052(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
1062(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
1072(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
1082(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
1092(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
10102(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
10112(CHAIN Q AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...Q9 - 236
1112(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R12 - 13
1122(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R15 - 25
1132(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R27 - 34
1142(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R35
1152(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
1162(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
1172(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
1182(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
1192(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
11102(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
11112(CHAIN R AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...R9 - 234
1212(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S12 - 13
1222(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S15 - 25
1232(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S27 - 34
1242(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S35
1252(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
1262(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
1272(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
1282(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
1292(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
12102(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
12112(CHAIN S AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...S9 - 236
1312(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T12 - 13
1322(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T15 - 25
1332(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T27 - 34
1342(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T35
1352(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
1362(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
1372(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
1382(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
1392(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
13102(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
13112(CHAIN T AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...T9 - 235
1412(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U12 - 13
1422(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U15 - 25
1432(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U27 - 34
1442(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U35
1452(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
1462(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
1472(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
1482(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
1492(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
14102(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235
14112(CHAIN U AND (RESSEQ 12:13 OR RESSEQ 15:25 OR RESSEQ...U9 - 235

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Proteasome subunit alpha / / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 25971.975 Da / Num. of mol.: 14 / Fragment: UNP residues 10-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, MRA_2124 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D5, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 25274.264 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, MRA_2125 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D6, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Chemical
ChemComp-7HZ / N-tert-butoxy-N~2~-(5-methyl-1,2-oxazole-3-carbonyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide


Type: Non-polymer / Class: Inhibitor / Mass: 553.607 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C28H35N5O7
References: N-tert-butoxy-N~2~-(5-methyl-1,2-oxazole-3-carbonyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2) and 14% PEG-3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 136892 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 71.0985836078 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 3.08→3.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.781 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.08356699278→49.8708274948 Å / SU ML: 0.316432552493 / Cross valid method: FREE R-VALUE / σ(F): 1.33703879814 / Phase error: 21.5532798867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.210710976933 6698 4.89412383639 %
Rwork0.18102232646 130160 -
obs0.182510984638 136858 98.10609319 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.4074637681 Å2
Refinement stepCycle: LAST / Resolution: 3.08356699278→49.8708274948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46367 0 560 92 47019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071705389294147628
X-RAY DIFFRACTIONf_angle_d0.7613789496164463
X-RAY DIFFRACTIONf_chiral_restr0.05137480725487286
X-RAY DIFFRACTIONf_plane_restr0.005277439918278470
X-RAY DIFFRACTIONf_dihedral_angle_d16.724278834928374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0836-3.11860.3580240178761560.2843970973613160X-RAY DIFFRACTION71.7904308292
3.1186-3.15530.3250092006312040.2776435052323862X-RAY DIFFRACTION88.2187025385
3.1553-3.19380.286807535672160.2745656036854107X-RAY DIFFRACTION92.2141638225
3.1938-3.23420.295950205122110.258887154514254X-RAY DIFFRACTION96.4988113248
3.2342-3.27670.2734153508822020.2595971924054330X-RAY DIFFRACTION98.2015167931
3.2767-3.32160.2861594508682260.2465474856134378X-RAY DIFFRACTION98.9681857266
3.3216-3.3690.2422023958922040.2312497921594402X-RAY DIFFRACTION99.5246326707
3.369-3.41930.2613534220172170.2359670110164418X-RAY DIFFRACTION99.7203098107
3.4193-3.47270.2745071538222400.2303519273584370X-RAY DIFFRACTION99.7403721333
3.4727-3.52970.2444327252952320.2189738107254404X-RAY DIFFRACTION99.8707453684
3.5297-3.59050.2314946617012480.2207900043274387X-RAY DIFFRACTION99.8707175178
3.5905-3.65580.2780718231852570.2334092107064371X-RAY DIFFRACTION99.9136442142
3.6558-3.72610.2686638097342140.230150855414402X-RAY DIFFRACTION99.8701860666
3.7261-3.80210.2508672100512030.1981284698114448X-RAY DIFFRACTION99.9140708915
3.8021-3.88470.1932988180692190.1889263199874432X-RAY DIFFRACTION99.935539321
3.8847-3.97510.2060476370292430.1868801562434376X-RAY DIFFRACTION99.8486813662
3.9751-4.07440.2196066365972090.1855390728414426X-RAY DIFFRACTION99.9568686651
4.0744-4.18450.221619150512200.1833078916634436X-RAY DIFFRACTION99.9141630901
4.1845-4.30760.198839313642660.1713894652354396X-RAY DIFFRACTION99.9356913183
4.3076-4.44660.2031615018432330.1653284196294390X-RAY DIFFRACTION99.9567567568
4.4466-4.60540.1768328726932150.1635598419474460X-RAY DIFFRACTION99.9358700299
4.6054-4.78960.1854711877712140.1498066640994422X-RAY DIFFRACTION100
4.7896-5.00740.1803517152342220.1500586122634419X-RAY DIFFRACTION100
5.0074-5.27120.1766810926862120.1526528101594464X-RAY DIFFRACTION99.9786187727
5.2712-5.6010.1956878024292060.1567443216714414X-RAY DIFFRACTION100
5.601-6.03280.1993085694342600.17458755934424X-RAY DIFFRACTION99.9786552828
6.0328-6.63860.2235580627352320.1710954500954444X-RAY DIFFRACTION99.9572466866
6.6386-7.59640.1739282475122340.1372417640164431X-RAY DIFFRACTION99.9785683669
7.5964-9.55960.1352588205022330.1089554354594456X-RAY DIFFRACTION100
9.5596-49.87730.1786235374852500.1598388760064477X-RAY DIFFRACTION99.3067226891

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