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- PDB-2vav: Crystal structure of deacetylcephalosporin C acetyltransferase (D... -

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Basic information

Entry
Database: PDB / ID: 2vav
TitleCrystal structure of deacetylcephalosporin C acetyltransferase (DAC-Soak)
ComponentsACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACETYL TRANSFERASE / A/B- HYDROLASE FOLD / ACYLTRANSFERASE / ACETYL COENZYME A / ANTIBIOTIC BIOSYNTHESIS / CEPHALOSPORIN BIOSYNTHESIS
Function / homology
Function and homology information


deacetylcephalosporin-C acetyltransferase / deacetylcephalosporin-C acetyltransferase activity / homoserine metabolic process / homoserine O-acetyltransferase activity / methionine biosynthetic process / antibiotic biosynthetic process
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CSC / Acetyl-CoA--deacetylcephalosporin C acetyltransferase
Similarity search - Component
Biological speciesACREMONIUM CHRYSOGENUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsLejon, S. / Ellis, J. / Valegard, K.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: The last step in cephalosporin C formation revealed: crystal structures of deacetylcephalosporin C acetyltransferase from Acremonium chrysogenum in complexes with reaction intermediates.
Authors: Lejon, S. / Ellis, J. / Valegard, K.
History
DepositionSep 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 12, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_validate_close_contact.label_alt_id_2
Revision 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,99939
Polymers591,11612
Non-polymers5,88327
Water8,989499
1
A: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
I: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6479
Polymers98,5192
Non-polymers1,1287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-36.1 kcal/mol
Surface area31430 Å2
MethodPISA
2
B: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
E: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5888
Polymers98,5192
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-27.2 kcal/mol
Surface area31400 Å2
MethodPISA
3
D: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
K: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4115
Polymers98,5192
Non-polymers8923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-22.5 kcal/mol
Surface area30590 Å2
MethodPISA
4
F: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
H: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4706
Polymers98,5192
Non-polymers9514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-31.7 kcal/mol
Surface area30520 Å2
MethodPISA
5
G: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
L: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4706
Polymers98,5192
Non-polymers9514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-22.4 kcal/mol
Surface area30250 Å2
MethodPISA
6
C: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
J: ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4115
Polymers98,5192
Non-polymers8923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-19.6 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.065, 108.865, 195.792
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L
14A
24B
34C
44D
54E
64F
74G
84H
94I
104J
114K
124L
15A
25B
35C
45D
55E
65F
75G
85H
95I
105J
115K
125L
16A
26B
36C
46D
56E
66F
76G
86H
96I
106J
116K
126L
17A
27B
37C
47D
57E
67F
77G
87H
97I
107J
117K
127L
18A
28B
38C
48D
58E
68F
78G
88H
98I
108J
118K
128L
19A
29B
39C
49D
59E
69F
79G
89H
99I
109J
119K
129L
110A
210B
310C
410D
510E
610F
710G
810H
910I
1010J
1110K
1210L
111A
211B
311C
411D
511E
611F
711G
811H
911I
1011J
1111K
1211L
112A
212B
312C
412D
512E
612F
712G
812H
912I
1012J
1112K
1212L
113A
213B
313C
413D
513E
613F
713G
813H
913I
1013J
1113K
1213L
114A
214B
314C
414D
514E
614F
714G
814H
914I
1014J
1114K
1214L
115A
215B
315C
415D
515E
615F
715G
815H
915I
1015J
1115K
1215L
116A
216B
316C
416D
516E
616F
716G
816H
916I
1016J
1116K
1216L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUAA7 - 3266 - 91
21ASNASNLEULEUBB7 - 3266 - 91
31ASNASNLEULEUCC7 - 3266 - 91
41ASNASNLEULEUDD7 - 3266 - 91
51ASNASNLEULEUEE7 - 3266 - 91
61ASNASNLEULEUFF7 - 3266 - 91
71ASNASNLEULEUGG7 - 3266 - 91
81ASNASNLEULEUHH7 - 3266 - 91
91ASNASNLEULEUII7 - 3266 - 91
101ASNASNLEULEUJJ7 - 3266 - 91
111ASNASNLEULEUKK7 - 3266 - 91
121ASNASNLEULEULL7 - 3266 - 91
12ASPASPSERSERAA34 - 4893 - 107
22ASPASPSERSERBB34 - 4893 - 107
32ASPASPSERSERCC34 - 4893 - 107
42ASPASPSERSERDD34 - 4893 - 107
52ASPASPSERSEREE34 - 4893 - 107
62ASPASPSERSERFF34 - 4893 - 107
72ASPASPSERSERGG34 - 4893 - 107
82ASPASPSERSERHH34 - 4893 - 107
92ASPASPSERSERII34 - 4893 - 107
102ASPASPSERSERJJ34 - 4893 - 107
112ASPASPSERSERKK34 - 4893 - 107
122ASPASPSERSERLL34 - 4893 - 107
13ASPASPPROPROAA50 - 119109 - 178
23ASPASPPROPROBB50 - 119109 - 178
33ASPASPPROPROCC50 - 119109 - 178
43ASPASPPROPRODD50 - 119109 - 178
53ASPASPPROPROEE50 - 119109 - 178
63ASPASPPROPROFF50 - 119109 - 178
73ASPASPPROPROGG50 - 119109 - 178
83ASPASPPROPROHH50 - 119109 - 178
93ASPASPPROPROII50 - 119109 - 178
103ASPASPPROPROJJ50 - 119109 - 178
113ASPASPPROPROKK50 - 119109 - 178
123ASPASPPROPROLL50 - 119109 - 178
14THRTHRVALVALAA121 - 127180 - 186
24THRTHRVALVALBB121 - 127180 - 186
34THRTHRVALVALCC121 - 127180 - 186
44THRTHRVALVALDD121 - 127180 - 186
54THRTHRVALVALEE121 - 127180 - 186
64THRTHRVALVALFF121 - 127180 - 186
74THRTHRVALVALGG121 - 127180 - 186
84THRTHRVALVALHH121 - 127180 - 186
94THRTHRVALVALII121 - 127180 - 186
104THRTHRVALVALJJ121 - 127180 - 186
114THRTHRVALVALKK121 - 127180 - 186
124THRTHRVALVALLL121 - 127180 - 186
15ILEILEHISHISAA129 - 130188 - 189
25ILEILEHISHISBB129 - 130188 - 189
35ILEILEHISHISCC129 - 130188 - 189
45ILEILEHISHISDD129 - 130188 - 189
55ILEILEHISHISEE129 - 130188 - 189
65ILEILEHISHISFF129 - 130188 - 189
75ILEILEHISHISGG129 - 130188 - 189
85ILEILEHISHISHH129 - 130188 - 189
95ILEILEHISHISII129 - 130188 - 189
105ILEILEHISHISJJ129 - 130188 - 189
115ILEILEHISHISKK129 - 130188 - 189
125ILEILEHISHISLL129 - 130188 - 189
16GLNGLNVALVALAA132 - 139191 - 198
26GLNGLNVALVALBB132 - 139191 - 198
36GLNGLNVALVALCC132 - 139191 - 198
46GLNGLNVALVALDD132 - 139191 - 198
56GLNGLNVALVALEE132 - 139191 - 198
66GLNGLNVALVALFF132 - 139191 - 198
76GLNGLNVALVALGG132 - 139191 - 198
86GLNGLNVALVALHH132 - 139191 - 198
96GLNGLNVALVALII132 - 139191 - 198
106GLNGLNVALVALJJ132 - 139191 - 198
116GLNGLNVALVALKK132 - 139191 - 198
126GLNGLNVALVALLL132 - 139191 - 198
17GLNGLNALAALAAA141 - 144200 - 203
27GLNGLNALAALABB141 - 144200 - 203
37GLNGLNALAALACC141 - 144200 - 203
47GLNGLNALAALADD141 - 144200 - 203
57GLNGLNALAALAEE141 - 144200 - 203
67GLNGLNALAALAFF141 - 144200 - 203
77GLNGLNALAALAGG141 - 144200 - 203
87GLNGLNALAALAHH141 - 144200 - 203
97GLNGLNALAALAII141 - 144200 - 203
107GLNGLNALAALAJJ141 - 144200 - 203
117GLNGLNALAALAKK141 - 144200 - 203
127GLNGLNALAALALL141 - 144200 - 203
18VALVALGLNGLNAA146 - 189205 - 248
28VALVALGLNGLNBB146 - 189205 - 248
38VALVALGLNGLNCC146 - 189205 - 248
48VALVALGLNGLNDD146 - 189205 - 248
58VALVALGLNGLNEE146 - 189205 - 248
68VALVALGLNGLNFF146 - 189205 - 248
78VALVALGLNGLNGG146 - 189205 - 248
88VALVALGLNGLNHH146 - 189205 - 248
98VALVALGLNGLNII146 - 189205 - 248
108VALVALGLNGLNJJ146 - 189205 - 248
118VALVALGLNGLNKK146 - 189205 - 248
128VALVALGLNGLNLL146 - 189205 - 248
19GLNGLNTYRTYRAA191 - 199250 - 258
29GLNGLNTYRTYRBB191 - 199250 - 258
39GLNGLNTYRTYRCC191 - 199250 - 258
49GLNGLNTYRTYRDD191 - 199250 - 258
59GLNGLNTYRTYREE191 - 199250 - 258
69GLNGLNTYRTYRFF191 - 199250 - 258
79GLNGLNTYRTYRGG191 - 199250 - 258
89GLNGLNTYRTYRHH191 - 199250 - 258
99GLNGLNTYRTYRII191 - 199250 - 258
109GLNGLNTYRTYRJJ191 - 199250 - 258
119GLNGLNTYRTYRKK191 - 199250 - 258
129GLNGLNTYRTYRLL191 - 199250 - 258
110GLYGLYALAALAAA202 - 217261 - 276
210GLYGLYALAALABB202 - 217261 - 276
310GLYGLYALAALACC202 - 217261 - 276
410GLYGLYALAALADD202 - 217261 - 276
510GLYGLYALAALAEE202 - 217261 - 276
610GLYGLYALAALAFF202 - 217261 - 276
710GLYGLYALAALAGG202 - 217261 - 276
810GLYGLYALAALAHH202 - 217261 - 276
910GLYGLYALAALAII202 - 217261 - 276
1010GLYGLYALAALAJJ202 - 217261 - 276
1110GLYGLYALAALAKK202 - 217261 - 276
1210GLYGLYALAALALL202 - 217261 - 276
111LYSLYSMETMETAA219 - 237278 - 296
211LYSLYSMETMETBB219 - 237278 - 296
311LYSLYSMETMETCC219 - 237278 - 296
411LYSLYSMETMETDD219 - 237278 - 296
511LYSLYSMETMETEE219 - 237278 - 296
611LYSLYSMETMETFF219 - 237278 - 296
711LYSLYSMETMETGG219 - 237278 - 296
811LYSLYSMETMETHH219 - 237278 - 296
911LYSLYSMETMETII219 - 237278 - 296
1011LYSLYSMETMETJJ219 - 237278 - 296
1111LYSLYSMETMETKK219 - 237278 - 296
1211LYSLYSMETMETLL219 - 237278 - 296
112PROPROTHRTHRAA270 - 303329 - 362
212PROPROTHRTHRBB270 - 303329 - 362
312PROPROTHRTHRCC270 - 303329 - 362
412PROPROTHRTHRDD270 - 303329 - 362
512PROPROTHRTHREE270 - 303329 - 362
612PROPROTHRTHRFF270 - 303329 - 362
712PROPROTHRTHRGG270 - 303329 - 362
812PROPROTHRTHRHH270 - 303329 - 362
912PROPROTHRTHRII270 - 303329 - 362
1012PROPROTHRTHRJJ270 - 303329 - 362
1112PROPROTHRTHRKK270 - 303329 - 362
1212PROPROTHRTHRLL270 - 303329 - 362
113HISHISSERSERAA304 - 307363 - 366
213HISHISSERSERBB304 - 307363 - 366
313HISHISSERSERCC304 - 307363 - 366
413HISHISSERSERDD304 - 307363 - 366
513HISHISSERSEREE304 - 307363 - 366
613HISHISSERSERFF304 - 307363 - 366
713HISHISSERSERGG304 - 307363 - 366
813HISHISSERSERHH304 - 307363 - 366
913HISHISSERSERII304 - 307363 - 366
1013HISHISSERSERJJ304 - 307363 - 366
1113HISHISSERSERKK304 - 307363 - 366
1213HISHISSERSERLL304 - 307363 - 366
114GLYGLYALAALAAA309 - 330368 - 389
214GLYGLYALAALABB309 - 330368 - 389
314GLYGLYALAALACC309 - 330368 - 389
414GLYGLYALAALADD309 - 330368 - 389
514GLYGLYALAALAEE309 - 330368 - 389
614GLYGLYALAALAFF309 - 330368 - 389
714GLYGLYALAALAGG309 - 330368 - 389
814GLYGLYALAALAHH309 - 330368 - 389
914GLYGLYALAALAII309 - 330368 - 389
1014GLYGLYALAALAJJ309 - 330368 - 389
1114GLYGLYALAALAKK309 - 330368 - 389
1214GLYGLYALAALALL309 - 330368 - 389
115SERSERASNASNAA332 - 359391 - 418
215SERSERASNASNBB332 - 359391 - 418
315SERSERASNASNCC332 - 359391 - 418
415SERSERASNASNDD332 - 359391 - 418
515SERSERASNASNEE332 - 359391 - 418
615SERSERASNASNFF332 - 359391 - 418
715SERSERASNASNGG332 - 359391 - 418
815SERSERASNASNHH332 - 359391 - 418
915SERSERASNASNII332 - 359391 - 418
1015SERSERASNASNJJ332 - 359391 - 418
1115SERSERASNASNKK332 - 359391 - 418
1215SERSERASNASNLL332 - 359391 - 418
116GLYGLYGLNGLNAA361 - 382420 - 441
216GLYGLYGLNGLNBB361 - 382420 - 441
316GLYGLYGLNGLNCC361 - 382420 - 441
416GLYGLYGLNGLNDD361 - 382420 - 441
516GLYGLYGLNGLNEE361 - 382420 - 441
616GLYGLYGLNGLNFF361 - 382420 - 441
716GLYGLYGLNGLNGG361 - 382420 - 441
816GLYGLYGLNGLNHH361 - 382420 - 441
916GLYGLYGLNGLNII361 - 382420 - 441
1016GLYGLYGLNGLNJJ361 - 382420 - 441
1116GLYGLYGLNGLNKK361 - 382420 - 441
1216GLYGLYGLNGLNLL361 - 382420 - 441

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

NCS oper:
IDCodeMatrixVector
1given(-0.9999, -0.007868, -0.007694), (0.00772, -0.9998, 0.01917), (-0.007843, 0.01911, 0.9998)152.9, 20.54, 0.4865
2given(-0.7937, 0.09822, -0.6004), (0.07438, 0.9951, 0.06448), (0.6038, 0.006523, -0.7971)147.8, 1.185, -19.53
3given(0.7935, -0.09857, -0.6005), (-0.07479, -0.9951, 0.06452), (-0.604, -0.006288, -0.797)58.1, -23.72, 168.8
4given(1, -0.000317, 3.4E-5), (-0.000317, -1, 0.000145), (3.4E-5, -0.000145, -1)61.05, 22.01, 97.9
5given(-0.5227, 0.5017, 0.6893), (0.3375, 0.8642, -0.3731), (-0.7828, 0.0376, -0.6211)110.5, -7.312, 56.3
6given(0.5331, 0.4925, 0.6879), (0.3799, -0.8659, 0.3254), (0.7559, 0.08787, -0.6487)-8.14, -43.33, 58.61
7given(0.5329, -0.4929, -0.6878), (0.3815, 0.8655, -0.3247), (0.7553, -0.08938, 0.6492)37.52, -53.93, -49.04
8given(-0.9999, 0.00861, 0.007416), (0.008462, 0.9998, -0.01974), (-0.007584, -0.01968, -0.9998)213, -0.1163, 99.23
9given(-0.8005, -0.09654, -0.5915), (-0.04778, 0.9941, -0.09757), (0.5975, -0.04984, -0.8004)157.4, 63.95, 41.78
10given(-0.8011, 0.09676, 0.5907), (-0.04842, -0.9941, 0.09717), (0.5966, 0.04924, 0.801)156.8, -28.94, -68.67
11given(-0.5226, -0.5019, -0.6892), (0.3375, -0.8641, 0.3733), (-0.7829, -0.03753, 0.621)220.9, -45.41, 44.09

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Components

#1: Protein
ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE / DCPC-ATF / DAC ACETYLTRANSFERASE / DAC-AT / DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE


Mass: 49259.664 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACREMONIUM CHRYSOGENUM (fungus) / Plasmid: PTWIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39058, deacetylcephalosporin-C acetyltransferase
#2: Chemical
ChemComp-CSC / 4-(3-ACETOXYMETHYL-2-CARBOXY-8-OXO-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-EN-7-YLCARBAMOYL)-1-CARBOXY-BUTYL-AMMONIUM / CEPHALOSPORIN C


Mass: 416.426 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H22N3O8S / Comment: antibiotic*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 18-19% PEG 4000, 0.1M IMIDAZOLE, 0.5M NACL, 0.2M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→109.11 Å / Num. obs: 177299 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→103.7 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.526 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 242-267 ARE DISORDERED. CEPHALOSPORIN C WAS MODELLED IN MULTIPLE CONFORMATIONS. ACETYLSERINE WAS MODELLED IN MULTIPLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3419 1.9 %RANDOM
Rwork0.219 ---
obs0.22 173708 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20.11 Å2
2--1.92 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.5→103.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32606 0 369 499 33474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02233846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.95445904
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26954131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39822.6931623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.719155315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.36515323
X-RAY DIFFRACTIONr_chiral_restr0.1130.24903
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.214673
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.223459
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.21301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.2258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.521052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.573233235
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.405314417
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9514.512629
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A194tight positional0.070.05
12B194tight positional0.080.05
13C194tight positional0.070.05
14D194tight positional0.070.05
15E194tight positional0.070.05
16F194tight positional0.060.05
17G194tight positional0.070.05
18H194tight positional0.080.05
19I194tight positional0.080.05
110J194tight positional0.080.05
111K194tight positional0.080.05
112L194tight positional0.060.05
21A119tight positional0.060.05
22B119tight positional0.060.05
23C119tight positional0.070.05
24D119tight positional0.070.05
25E119tight positional0.060.05
26F119tight positional0.080.05
27G119tight positional0.070.05
28H119tight positional0.070.05
29I119tight positional0.060.05
210J119tight positional0.070.05
211K119tight positional0.070.05
212L119tight positional0.080.05
31A483tight positional0.060.05
32B483tight positional0.050.05
33C483tight positional0.080.05
34D483tight positional0.080.05
35E483tight positional0.060.05
36F483tight positional0.070.05
37G483tight positional0.070.05
38H483tight positional0.070.05
39I483tight positional0.050.05
310J483tight positional0.080.05
311K483tight positional0.080.05
312L483tight positional0.070.05
41A56tight positional0.070.05
42B56tight positional0.060.05
43C56tight positional0.050.05
44D56tight positional0.050.05
45E56tight positional0.070.05
46F56tight positional0.070.05
47G56tight positional0.060.05
48H56tight positional0.060.05
49I56tight positional0.070.05
410J56tight positional0.080.05
411K56tight positional0.080.05
412L56tight positional0.060.05
51A18tight positional0.050.05
52B18tight positional0.030.05
53C18tight positional0.050.05
54D18tight positional0.050.05
55E18tight positional0.050.05
56F18tight positional0.040.05
57G18tight positional0.040.05
58H18tight positional0.040.05
59I18tight positional0.040.05
510J18tight positional0.070.05
511K18tight positional0.080.05
512L18tight positional0.050.05
61A62tight positional0.060.05
62B62tight positional0.060.05
63C62tight positional0.070.05
64D62tight positional0.080.05
65E62tight positional0.060.05
66F62tight positional0.070.05
67G62tight positional0.10.05
68H62tight positional0.060.05
69I62tight positional0.060.05
610J62tight positional0.080.05
611K62tight positional0.080.05
612L62tight positional0.070.05
71A27tight positional0.060.05
72B27tight positional0.040.05
73C27tight positional0.070.05
74D27tight positional0.050.05
75E27tight positional0.050.05
76F27tight positional0.040.05
77G27tight positional0.070.05
78H27tight positional0.070.05
79I27tight positional0.040.05
710J27tight positional0.060.05
711K27tight positional0.060.05
712L27tight positional0.040.05
81A350tight positional0.070.05
82B350tight positional0.060.05
83C350tight positional0.070.05
84D350tight positional0.070.05
85E350tight positional0.060.05
86F350tight positional0.060.05
87G350tight positional0.080.05
88H350tight positional0.090.05
89I350tight positional0.070.05
810J350tight positional0.080.05
811K350tight positional0.080.05
812L350tight positional0.060.05
91A79tight positional0.040.05
92B79tight positional0.050.05
93C79tight positional0.050.05
94D79tight positional0.050.05
95E79tight positional0.050.05
96F79tight positional0.060.05
97G79tight positional0.050.05
98H79tight positional0.050.05
99I79tight positional0.060.05
910J79tight positional0.060.05
911K79tight positional0.060.05
912L79tight positional0.050.05
101A123tight positional0.060.05
102B123tight positional0.050.05
103C123tight positional0.050.05
104D123tight positional0.050.05
105E123tight positional0.060.05
106F123tight positional0.050.05
107G123tight positional0.050.05
108H123tight positional0.050.05
109I123tight positional0.050.05
1010J123tight positional0.060.05
1011K123tight positional0.060.05
1012L123tight positional0.040.05
111A158tight positional0.080.05
112B158tight positional0.050.05
113C158tight positional0.060.05
114D158tight positional0.060.05
115E158tight positional0.080.05
116F158tight positional0.070.05
117G158tight positional0.060.05
118H158tight positional0.060.05
119I158tight positional0.060.05
1110J158tight positional0.060.05
1111K158tight positional0.060.05
1112L158tight positional0.060.05
121A271tight positional0.070.05
122B271tight positional0.060.05
123C271tight positional0.080.05
124D271tight positional0.080.05
125E271tight positional0.070.05
126F271tight positional0.070.05
127G271tight positional0.080.05
128H271tight positional0.080.05
129I271tight positional0.060.05
1210J271tight positional0.070.05
1211K271tight positional0.070.05
1212L271tight positional0.070.05
131A32tight positional0.060.05
132B32tight positional0.050.05
133C32tight positional0.060.05
134D32tight positional0.050.05
135E32tight positional0.060.05
136F32tight positional0.050.05
137G32tight positional0.050.05
138H32tight positional0.050.05
139I32tight positional0.060.05
1310J32tight positional0.10.05
1311K32tight positional0.110.05
1312L32tight positional0.060.05
141A151tight positional0.080.05
142B151tight positional0.070.05
143C151tight positional0.050.05
144D151tight positional0.110.05
145E151tight positional0.070.05
146F151tight positional0.060.05
147G151tight positional0.070.05
148H151tight positional0.070.05
149I151tight positional0.060.05
1410J151tight positional0.070.05
1411K151tight positional0.070.05
1412L151tight positional0.060.05
151A210tight positional0.070.05
152B210tight positional0.060.05
153C210tight positional0.070.05
154D210tight positional0.070.05
155E210tight positional0.070.05
156F210tight positional0.060.05
157G210tight positional0.050.05
158H210tight positional0.050.05
159I210tight positional0.060.05
1510J210tight positional0.060.05
1511K210tight positional0.060.05
1512L210tight positional0.070.05
161A176tight positional0.060.05
162B176tight positional0.070.05
163C176tight positional0.060.05
164D176tight positional0.060.05
165E176tight positional0.060.05
166F176tight positional0.060.05
167G176tight positional0.060.05
168H176tight positional0.060.05
169I176tight positional0.070.05
1610J176tight positional0.070.05
1611K176tight positional0.070.05
1612L176tight positional0.060.05
11A194tight thermal0.280.5
12B194tight thermal0.310.5
13C194tight thermal0.220.5
14D194tight thermal0.220.5
15E194tight thermal0.270.5
16F194tight thermal0.250.5
17G194tight thermal0.140.5
18H194tight thermal0.130.5
19I194tight thermal0.30.5
110J194tight thermal0.490.5
111K194tight thermal0.490.5
112L194tight thermal0.250.5
21A119tight thermal0.190.5
22B119tight thermal0.220.5
23C119tight thermal0.250.5
24D119tight thermal0.240.5
25E119tight thermal0.190.5
26F119tight thermal0.20.5
27G119tight thermal0.210.5
28H119tight thermal0.210.5
29I119tight thermal0.20.5
210J119tight thermal0.440.5
211K119tight thermal0.440.5
212L119tight thermal0.220.5
31A483tight thermal0.190.5
32B483tight thermal0.240.5
33C483tight thermal0.240.5
34D483tight thermal0.250.5
35E483tight thermal0.190.5
36F483tight thermal0.190.5
37G483tight thermal0.170.5
38H483tight thermal0.160.5
39I483tight thermal0.240.5
310J483tight thermal0.470.5
311K483tight thermal0.470.5
312L483tight thermal0.180.5
41A56tight thermal0.340.5
42B56tight thermal0.310.5
43C56tight thermal0.30.5
44D56tight thermal0.310.5
45E56tight thermal0.320.5
46F56tight thermal0.230.5
47G56tight thermal0.190.5
48H56tight thermal0.170.5
49I56tight thermal0.340.5
410J56tight thermal0.660.5
411K56tight thermal0.70.5
412L56tight thermal0.240.5
51A18tight thermal0.260.5
52B18tight thermal0.40.5
53C18tight thermal0.380.5
54D18tight thermal0.350.5
55E18tight thermal0.310.5
56F18tight thermal0.250.5
57G18tight thermal0.230.5
58H18tight thermal0.160.5
59I18tight thermal0.380.5
510J18tight thermal0.770.5
511K18tight thermal0.770.5
512L18tight thermal0.30.5
61A62tight thermal0.190.5
62B62tight thermal0.320.5
63C62tight thermal0.220.5
64D62tight thermal0.220.5
65E62tight thermal0.20.5
66F62tight thermal0.20.5
67G62tight thermal0.130.5
68H62tight thermal0.150.5
69I62tight thermal0.30.5
610J62tight thermal0.50.5
611K62tight thermal0.50.5
612L62tight thermal0.170.5
71A27tight thermal0.170.5
72B27tight thermal0.260.5
73C27tight thermal0.210.5
74D27tight thermal0.180.5
75E27tight thermal0.190.5
76F27tight thermal0.180.5
77G27tight thermal0.190.5
78H27tight thermal0.210.5
79I27tight thermal0.240.5
710J27tight thermal0.410.5
711K27tight thermal0.460.5
712L27tight thermal0.150.5
81A350tight thermal0.20.5
82B350tight thermal0.250.5
83C350tight thermal0.190.5
84D350tight thermal0.180.5
85E350tight thermal0.190.5
86F350tight thermal0.170.5
87G350tight thermal0.180.5
88H350tight thermal0.190.5
89I350tight thermal0.240.5
810J350tight thermal0.470.5
811K350tight thermal0.460.5
812L350tight thermal0.180.5
91A79tight thermal0.220.5
92B79tight thermal0.20.5
93C79tight thermal0.160.5
94D79tight thermal0.150.5
95E79tight thermal0.210.5
96F79tight thermal0.170.5
97G79tight thermal0.130.5
98H79tight thermal0.140.5
99I79tight thermal0.210.5
910J79tight thermal0.330.5
911K79tight thermal0.330.5
912L79tight thermal0.170.5
101A123tight thermal0.140.5
102B123tight thermal0.170.5
103C123tight thermal0.130.5
104D123tight thermal0.120.5
105E123tight thermal0.20.5
106F123tight thermal0.120.5
107G123tight thermal0.130.5
108H123tight thermal0.120.5
109I123tight thermal0.180.5
1010J123tight thermal0.240.5
1011K123tight thermal0.240.5
1012L123tight thermal0.130.5
111A158tight thermal0.210.5
112B158tight thermal0.190.5
113C158tight thermal0.260.5
114D158tight thermal0.250.5
115E158tight thermal0.190.5
116F158tight thermal0.170.5
117G158tight thermal0.150.5
118H158tight thermal0.150.5
119I158tight thermal0.210.5
1110J158tight thermal0.170.5
1111K158tight thermal0.160.5
1112L158tight thermal0.170.5
121A271tight thermal0.190.5
122B271tight thermal0.220.5
123C271tight thermal0.20.5
124D271tight thermal0.210.5
125E271tight thermal0.190.5
126F271tight thermal0.180.5
127G271tight thermal0.150.5
128H271tight thermal0.140.5
129I271tight thermal0.220.5
1210J271tight thermal0.350.5
1211K271tight thermal0.360.5
1212L271tight thermal0.170.5
131A32tight thermal0.270.5
132B32tight thermal0.290.5
133C32tight thermal0.230.5
134D32tight thermal0.220.5
135E32tight thermal0.260.5
136F32tight thermal0.190.5
137G32tight thermal0.130.5
138H32tight thermal0.120.5
139I32tight thermal0.340.5
1310J32tight thermal0.550.5
1311K32tight thermal0.570.5
1312L32tight thermal0.190.5
141A151tight thermal0.190.5
142B151tight thermal0.230.5
143C151tight thermal0.180.5
144D151tight thermal0.170.5
145E151tight thermal0.180.5
146F151tight thermal0.150.5
147G151tight thermal0.150.5
148H151tight thermal0.150.5
149I151tight thermal0.230.5
1410J151tight thermal0.390.5
1411K151tight thermal0.410.5
1412L151tight thermal0.150.5
151A210tight thermal0.140.5
152B210tight thermal0.180.5
153C210tight thermal0.150.5
154D210tight thermal0.150.5
155E210tight thermal0.140.5
156F210tight thermal0.170.5
157G210tight thermal0.150.5
158H210tight thermal0.140.5
159I210tight thermal0.170.5
1510J210tight thermal0.280.5
1511K210tight thermal0.290.5
1512L210tight thermal0.160.5
161A176tight thermal0.130.5
162B176tight thermal0.210.5
163C176tight thermal0.150.5
164D176tight thermal0.140.5
165E176tight thermal0.140.5
166F176tight thermal0.170.5
167G176tight thermal0.140.5
168H176tight thermal0.140.5
169I176tight thermal0.20.5
1610J176tight thermal0.270.5
1611K176tight thermal0.270.5
1612L176tight thermal0.170.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.295 13037
Rfree-0

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