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- PDB-7kel: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kel
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DIHYDRODIPICOLINATE SYNTHASE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaran, S. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site
Authors: Yazdi, M.M. / Saran, S. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,274112
Polymers410,11612
Non-polymers7,158100
Water28,3201572
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,62922
Polymers68,3532
Non-polymers1,27720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-1 kcal/mol
Surface area21900 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,94524
Polymers68,3532
Non-polymers1,59222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint15 kcal/mol
Surface area22170 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22214
Polymers68,3532
Non-polymers86912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-8 kcal/mol
Surface area22450 Å2
MethodPISA
4
E: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,19214
Polymers68,3532
Non-polymers83912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-26 kcal/mol
Surface area22550 Å2
MethodPISA
5
H: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,56619
Polymers68,3532
Non-polymers1,21317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-4 kcal/mol
Surface area21380 Å2
MethodPISA
6
I: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,72019
Polymers68,3532
Non-polymers1,36717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint5 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.880, 201.440, 113.660
Angle α, β, γ (deg.)90.000, 108.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5:17 or resid 19:20 or resid...
21(chain B and (resid 5:17 or resid 19:20 or resid...
31(chain C and (resid 5:17 or resid 19:20 or resid...
41(chain D and (resid 5:17 or resid 19:20 or resid...
51(chain E and (resid 5:17 or resid 19:20 or resid...
61(chain F and (resid 5:17 or resid 19:20 or resid...
71(chain G and (resid 5:17 or resid 19:20 or resid...
81(chain H and (resid 5:17 or resid 19:20 or resid...
91(chain I and (resid 5:17 or resid 19:20 or resid...
101(chain J and (resid 5:17 or resid 19:20 or resid...
111(chain K and (resid 5:17 or resid 19:20 or resid...
121(chain L and (resid 5:17 or resid 19:20 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5:17 or resid 19:20 or resid...A5 - 17
121(chain A and (resid 5:17 or resid 19:20 or resid...A19 - 20
131(chain A and (resid 5:17 or resid 19:20 or resid...A22 - 24
141(chain A and (resid 5:17 or resid 19:20 or resid...A26 - 28
151(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 31
161(chain A and (resid 5:17 or resid 19:20 or resid...A33 - 55
171(chain A and (resid 5:17 or resid 19:20 or resid...A58 - 59
181(chain A and (resid 5:17 or resid 19:20 or resid...A61 - 67
191(chain A and (resid 5:17 or resid 19:20 or resid...A69 - 70
1101(chain A and (resid 5:17 or resid 19:20 or resid...A72 - 73
1111(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1121(chain A and (resid 5:17 or resid 19:20 or resid...A78 - 86
1131(chain A and (resid 5:17 or resid 19:20 or resid...A86 - 94
1141(chain A and (resid 5:17 or resid 19:20 or resid...A99 - 97
1151(chain A and (resid 5:17 or resid 19:20 or resid...A91 - 127
1161(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1171(chain A and (resid 5:17 or resid 19:20 or resid...A167 - 183
1181(chain A and (resid 5:17 or resid 19:20 or resid...A236 - 264
1191(chain A and (resid 5:17 or resid 19:20 or resid...A236 - 266
1201(chain A and (resid 5:17 or resid 19:20 or resid...A268 - 279
1211(chain A and (resid 5:17 or resid 19:20 or resid...A282 - 287
1221(chain A and (resid 5:17 or resid 19:20 or resid...A293
1231(chain A and (resid 5:17 or resid 19:20 or resid...A298
1241(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1251(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1261(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1271(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1281(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1291(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1301(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1311(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
1321(chain A and (resid 5:17 or resid 19:20 or resid...A4 - 298
211(chain B and (resid 5:17 or resid 19:20 or resid...B5 - 17
221(chain B and (resid 5:17 or resid 19:20 or resid...B19 - 20
231(chain B and (resid 5:17 or resid 19:20 or resid...B22 - 24
241(chain B and (resid 5:17 or resid 19:20 or resid...B26 - 28
251(chain B and (resid 5:17 or resid 19:20 or resid...B33 - 55
261(chain B and (resid 5:17 or resid 19:20 or resid...B58 - 59
271(chain B and (resid 5:17 or resid 19:20 or resid...B61 - 67
281(chain B and (resid 5:17 or resid 19:20 or resid...B69 - 70
291(chain B and (resid 5:17 or resid 19:20 or resid...B72 - 73
2101(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2111(chain B and (resid 5:17 or resid 19:20 or resid...B88 - 86
2121(chain B and (resid 5:17 or resid 19:20 or resid...B96 - 94
2131(chain B and (resid 5:17 or resid 19:20 or resid...B99 - 97
2141(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2151(chain B and (resid 5:17 or resid 19:20 or resid...B161 - 165
2161(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2171(chain B and (resid 5:17 or resid 19:20 or resid...B167 - 183
2181(chain B and (resid 5:17 or resid 19:20 or resid...B185 - 230
2191(chain B and (resid 5:17 or resid 19:20 or resid...B236 - 266
2201(chain B and (resid 5:17 or resid 19:20 or resid...B268 - 27
2211(chain B and (resid 5:17 or resid 19:20 or resid...B282 - 287
2221(chain B and (resid 5:17 or resid 19:20 or resid...B289 - 290
2231(chain B and (resid 5:17 or resid 19:20 or resid...B293
2241(chain B and (resid 5:17 or resid 19:20 or resid...B295 - 297
2251(chain B and (resid 5:17 or resid 19:20 or resid...B298
2261(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2271(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2281(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2291(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2301(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2311(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
2321(chain B and (resid 5:17 or resid 19:20 or resid...B3 - 298
311(chain C and (resid 5:17 or resid 19:20 or resid...C5 - 17
321(chain C and (resid 5:17 or resid 19:20 or resid...C19 - 20
331(chain C and (resid 5:17 or resid 19:20 or resid...C22 - 24
341(chain C and (resid 5:17 or resid 19:20 or resid...C26 - 28
351(chain C and (resid 5:17 or resid 19:20 or resid...C33 - 55
361(chain C and (resid 5:17 or resid 19:20 or resid...C58 - 59
371(chain C and (resid 5:17 or resid 19:20 or resid...C61 - 67
381(chain C and (resid 5:17 or resid 19:20 or resid...C69 - 70
391(chain C and (resid 5:17 or resid 19:20 or resid...C72 - 73
3101(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3111(chain C and (resid 5:17 or resid 19:20 or resid...C88 - 86
3121(chain C and (resid 5:17 or resid 19:20 or resid...C96 - 94
3131(chain C and (resid 5:17 or resid 19:20 or resid...C99 - 97
3141(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3151(chain C and (resid 5:17 or resid 19:20 or resid...C161 - 165
3161(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3171(chain C and (resid 5:17 or resid 19:20 or resid...C167 - 183
3181(chain C and (resid 5:17 or resid 19:20 or resid...C185 - 230
3191(chain C and (resid 5:17 or resid 19:20 or resid...C236 - 266
3201(chain C and (resid 5:17 or resid 19:20 or resid...C268 - 27
3211(chain C and (resid 5:17 or resid 19:20 or resid...C282 - 287
3221(chain C and (resid 5:17 or resid 19:20 or resid...C289 - 290
3231(chain C and (resid 5:17 or resid 19:20 or resid...C293
3241(chain C and (resid 5:17 or resid 19:20 or resid...C295 - 297
3251(chain C and (resid 5:17 or resid 19:20 or resid...C298
3261(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3271(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3281(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3291(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3301(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3311(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
3321(chain C and (resid 5:17 or resid 19:20 or resid...C3 - 298
411(chain D and (resid 5:17 or resid 19:20 or resid...D5 - 17
421(chain D and (resid 5:17 or resid 19:20 or resid...D19 - 20
431(chain D and (resid 5:17 or resid 19:20 or resid...D22 - 24
441(chain D and (resid 5:17 or resid 19:20 or resid...D33 - 55
451(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 31
461(chain D and (resid 5:17 or resid 19:20 or resid...D58 - 59
471(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 67
481(chain D and (resid 5:17 or resid 19:20 or resid...D69 - 70
491(chain D and (resid 5:17 or resid 19:20 or resid...D0
4101(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 298
4111(chain D and (resid 5:17 or resid 19:20 or resid...D77 - 86
4121(chain D and (resid 5:17 or resid 19:20 or resid...D96 - 97
4131(chain D and (resid 5:17 or resid 19:20 or resid...D99
4141(chain D and (resid 5:17 or resid 19:20 or resid...D129 - 159
4151(chain D and (resid 5:17 or resid 19:20 or resid...D167 - 183
4161(chain D and (resid 5:17 or resid 19:20 or resid...D185 - 2
4171(chain D and (resid 5:17 or resid 19:20 or resid...D2330
4181(chain D and (resid 5:17 or resid 19:20 or resid...D4 - 298
4191(chain D and (resid 5:17 or resid 19:20 or resid...D282 - 287
4201(chain D and (resid 5:17 or resid 19:20 or resid...D293
4211(chain D and (resid 5:17 or resid 19:20 or resid...D295 - 2
511(chain E and (resid 5:17 or resid 19:20 or resid...E5 - 17
521(chain E and (resid 5:17 or resid 19:20 or resid...E19 - 20
531(chain E and (resid 5:17 or resid 19:20 or resid...E22 - 24
541(chain E and (resid 5:17 or resid 19:20 or resid...E26 - 28
551(chain E and (resid 5:17 or resid 19:20 or resid...E33 - 55
561(chain E and (resid 5:17 or resid 19:20 or resid...E58 - 59
571(chain E and (resid 5:17 or resid 19:20 or resid...E61 - 67
581(chain E and (resid 5:17 or resid 19:20 or resid...E69 - 70
591(chain E and (resid 5:17 or resid 19:20 or resid...E72 - 73
5101(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5111(chain E and (resid 5:17 or resid 19:20 or resid...E88 - 86
5121(chain E and (resid 5:17 or resid 19:20 or resid...E96 - 94
5131(chain E and (resid 5:17 or resid 19:20 or resid...E99 - 97
5141(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5151(chain E and (resid 5:17 or resid 19:20 or resid...E161 - 165
5161(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5171(chain E and (resid 5:17 or resid 19:20 or resid...E167 - 183
5181(chain E and (resid 5:17 or resid 19:20 or resid...E185 - 230
5191(chain E and (resid 5:17 or resid 19:20 or resid...E236 - 266
5201(chain E and (resid 5:17 or resid 19:20 or resid...E268 - 27
5211(chain E and (resid 5:17 or resid 19:20 or resid...E282 - 287
5221(chain E and (resid 5:17 or resid 19:20 or resid...E289 - 290
5231(chain E and (resid 5:17 or resid 19:20 or resid...E293
5241(chain E and (resid 5:17 or resid 19:20 or resid...E295 - 297
5251(chain E and (resid 5:17 or resid 19:20 or resid...E298
5261(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5271(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5281(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5291(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5301(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5311(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
5321(chain E and (resid 5:17 or resid 19:20 or resid...E4 - 298
611(chain F and (resid 5:17 or resid 19:20 or resid...F5 - 17
621(chain F and (resid 5:17 or resid 19:20 or resid...F19 - 20
631(chain F and (resid 5:17 or resid 19:20 or resid...F22 - 24
641(chain F and (resid 5:17 or resid 19:20 or resid...F33 - 55
651(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 31
661(chain F and (resid 5:17 or resid 19:20 or resid...F58 - 59
671(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 67
681(chain F and (resid 5:17 or resid 19:20 or resid...F69 - 70
691(chain F and (resid 5:17 or resid 19:20 or resid...F0
6101(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 298
6111(chain F and (resid 5:17 or resid 19:20 or resid...F77 - 86
6121(chain F and (resid 5:17 or resid 19:20 or resid...F96 - 97
6131(chain F and (resid 5:17 or resid 19:20 or resid...F99
6141(chain F and (resid 5:17 or resid 19:20 or resid...F129 - 159
6151(chain F and (resid 5:17 or resid 19:20 or resid...F167 - 183
6161(chain F and (resid 5:17 or resid 19:20 or resid...F185 - 2
6171(chain F and (resid 5:17 or resid 19:20 or resid...F2330
6181(chain F and (resid 5:17 or resid 19:20 or resid...F3 - 298
6191(chain F and (resid 5:17 or resid 19:20 or resid...F282 - 287
6201(chain F and (resid 5:17 or resid 19:20 or resid...F293
6211(chain F and (resid 5:17 or resid 19:20 or resid...F295 - 2
711(chain G and (resid 5:17 or resid 19:20 or resid...G5 - 17
721(chain G and (resid 5:17 or resid 19:20 or resid...G19 - 20
731(chain G and (resid 5:17 or resid 19:20 or resid...G22 - 24
741(chain G and (resid 5:17 or resid 19:20 or resid...G33 - 55
751(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 31
761(chain G and (resid 5:17 or resid 19:20 or resid...G58 - 59
771(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 67
781(chain G and (resid 5:17 or resid 19:20 or resid...G69 - 70
791(chain G and (resid 5:17 or resid 19:20 or resid...G0
7101(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 298
7111(chain G and (resid 5:17 or resid 19:20 or resid...G77 - 86
7121(chain G and (resid 5:17 or resid 19:20 or resid...G96 - 97
7131(chain G and (resid 5:17 or resid 19:20 or resid...G99
7141(chain G and (resid 5:17 or resid 19:20 or resid...G129 - 159
7151(chain G and (resid 5:17 or resid 19:20 or resid...G167 - 183
7161(chain G and (resid 5:17 or resid 19:20 or resid...G185 - 2
7171(chain G and (resid 5:17 or resid 19:20 or resid...G2330
7181(chain G and (resid 5:17 or resid 19:20 or resid...G3 - 298
7191(chain G and (resid 5:17 or resid 19:20 or resid...G282 - 287
7201(chain G and (resid 5:17 or resid 19:20 or resid...G293
7211(chain G and (resid 5:17 or resid 19:20 or resid...G295 - 2
811(chain H and (resid 5:17 or resid 19:20 or resid...H5 - 17
821(chain H and (resid 5:17 or resid 19:20 or resid...H19 - 20
831(chain H and (resid 5:17 or resid 19:20 or resid...H22 - 24
841(chain H and (resid 5:17 or resid 19:20 or resid...H33 - 55
851(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 31
861(chain H and (resid 5:17 or resid 19:20 or resid...H58 - 59
871(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 67
881(chain H and (resid 5:17 or resid 19:20 or resid...H69 - 70
891(chain H and (resid 5:17 or resid 19:20 or resid...H0
8101(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 298
8111(chain H and (resid 5:17 or resid 19:20 or resid...H77 - 86
8121(chain H and (resid 5:17 or resid 19:20 or resid...H96 - 97
8131(chain H and (resid 5:17 or resid 19:20 or resid...H99
8141(chain H and (resid 5:17 or resid 19:20 or resid...H129 - 159
8151(chain H and (resid 5:17 or resid 19:20 or resid...H167 - 183
8161(chain H and (resid 5:17 or resid 19:20 or resid...H185 - 2
8171(chain H and (resid 5:17 or resid 19:20 or resid...H2330
8181(chain H and (resid 5:17 or resid 19:20 or resid...H3 - 298
8191(chain H and (resid 5:17 or resid 19:20 or resid...H282 - 287
8201(chain H and (resid 5:17 or resid 19:20 or resid...H293
8211(chain H and (resid 5:17 or resid 19:20 or resid...H295 - 2
911(chain I and (resid 5:17 or resid 19:20 or resid...I5 - 17
921(chain I and (resid 5:17 or resid 19:20 or resid...I19 - 20
931(chain I and (resid 5:17 or resid 19:20 or resid...I22 - 24
941(chain I and (resid 5:17 or resid 19:20 or resid...I33 - 55
951(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 31
961(chain I and (resid 5:17 or resid 19:20 or resid...I58 - 59
971(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 67
981(chain I and (resid 5:17 or resid 19:20 or resid...I69 - 70
991(chain I and (resid 5:17 or resid 19:20 or resid...I0
9101(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9111(chain I and (resid 5:17 or resid 19:20 or resid...I77 - 86
9121(chain I and (resid 5:17 or resid 19:20 or resid...I96 - 97
9131(chain I and (resid 5:17 or resid 19:20 or resid...I99
9141(chain I and (resid 5:17 or resid 19:20 or resid...I129 - 159
9151(chain I and (resid 5:17 or resid 19:20 or resid...I167 - 183
9161(chain I and (resid 5:17 or resid 19:20 or resid...I185 - 2
9171(chain I and (resid 5:17 or resid 19:20 or resid...I2330
9181(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9191(chain I and (resid 5:17 or resid 19:20 or resid...I282 - 287
9201(chain I and (resid 5:17 or resid 19:20 or resid...I293
9211(chain I and (resid 5:17 or resid 19:20 or resid...I298
9221(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9231(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9241(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9251(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9261(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9271(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9281(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9291(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9301(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9311(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
9321(chain I and (resid 5:17 or resid 19:20 or resid...I3 - 298
1011(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 17
1021(chain J and (resid 5:17 or resid 19:20 or resid...J19 - 20
1031(chain J and (resid 5:17 or resid 19:20 or resid...J22 - 24
1041(chain J and (resid 5:17 or resid 19:20 or resid...J33 - 55
1051(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 31
1061(chain J and (resid 5:17 or resid 19:20 or resid...J58 - 59
1071(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 67
1081(chain J and (resid 5:17 or resid 19:20 or resid...J69 - 70
1091(chain J and (resid 5:17 or resid 19:20 or resid...J0
10101(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10111(chain J and (resid 5:17 or resid 19:20 or resid...J77 - 86
10121(chain J and (resid 5:17 or resid 19:20 or resid...J96 - 97
10131(chain J and (resid 5:17 or resid 19:20 or resid...J99
10141(chain J and (resid 5:17 or resid 19:20 or resid...J129 - 159
10151(chain J and (resid 5:17 or resid 19:20 or resid...J167 - 183
10161(chain J and (resid 5:17 or resid 19:20 or resid...J185 - 2
10171(chain J and (resid 5:17 or resid 19:20 or resid...J2330
10181(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10191(chain J and (resid 5:17 or resid 19:20 or resid...J282 - 287
10201(chain J and (resid 5:17 or resid 19:20 or resid...J293
10211(chain J and (resid 5:17 or resid 19:20 or resid...J298
10221(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10231(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10241(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10251(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10261(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10271(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10281(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10291(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10301(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10311(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
10321(chain J and (resid 5:17 or resid 19:20 or resid...J5 - 298
1111(chain K and (resid 5:17 or resid 19:20 or resid...K5 - 17
1121(chain K and (resid 5:17 or resid 19:20 or resid...K19 - 20
1131(chain K and (resid 5:17 or resid 19:20 or resid...K22 - 24
1141(chain K and (resid 5:17 or resid 19:20 or resid...K33 - 55
1151(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 31
1161(chain K and (resid 5:17 or resid 19:20 or resid...K58 - 59
1171(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 67
1181(chain K and (resid 5:17 or resid 19:20 or resid...K69 - 70
1191(chain K and (resid 5:17 or resid 19:20 or resid...K0
11101(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 298
11111(chain K and (resid 5:17 or resid 19:20 or resid...K77 - 86
11121(chain K and (resid 5:17 or resid 19:20 or resid...K96 - 97
11131(chain K and (resid 5:17 or resid 19:20 or resid...K99
11141(chain K and (resid 5:17 or resid 19:20 or resid...K129 - 159
11151(chain K and (resid 5:17 or resid 19:20 or resid...K167 - 183
11161(chain K and (resid 5:17 or resid 19:20 or resid...K185 - 2
11171(chain K and (resid 5:17 or resid 19:20 or resid...K2330
11181(chain K and (resid 5:17 or resid 19:20 or resid...K3 - 298
11191(chain K and (resid 5:17 or resid 19:20 or resid...K282 - 287
11201(chain K and (resid 5:17 or resid 19:20 or resid...K293
11211(chain K and (resid 5:17 or resid 19:20 or resid...K295 - 2
1211(chain L and (resid 5:17 or resid 19:20 or resid...L5 - 17
1221(chain L and (resid 5:17 or resid 19:20 or resid...L19 - 20
1231(chain L and (resid 5:17 or resid 19:20 or resid...L22 - 24
1241(chain L and (resid 5:17 or resid 19:20 or resid...L33 - 55
1251(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 31
1261(chain L and (resid 5:17 or resid 19:20 or resid...L58 - 59
1271(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 67
1281(chain L and (resid 5:17 or resid 19:20 or resid...L69 - 70
1291(chain L and (resid 5:17 or resid 19:20 or resid...L0
12101(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 298
12111(chain L and (resid 5:17 or resid 19:20 or resid...L77 - 86
12121(chain L and (resid 5:17 or resid 19:20 or resid...L96 - 97
12131(chain L and (resid 5:17 or resid 19:20 or resid...L99
12141(chain L and (resid 5:17 or resid 19:20 or resid...L129 - 159
12151(chain L and (resid 5:17 or resid 19:20 or resid...L167 - 183
12161(chain L and (resid 5:17 or resid 19:20 or resid...L185 - 2
12171(chain L and (resid 5:17 or resid 19:20 or resid...L2330
12181(chain L and (resid 5:17 or resid 19:20 or resid...L3 - 298
12191(chain L and (resid 5:17 or resid 19:20 or resid...L282 - 287
12201(chain L and (resid 5:17 or resid 19:20 or resid...L293
12211(chain L and (resid 5:17 or resid 19:20 or resid...L295 - 2

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34176.293 Da / Num. of mol.: 12 / Mutation: H59K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dapA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U0QMK8, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 7 types, 1672 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→38.583 Å / Num. obs: 204501 / % possible obs: 99.6 % / Redundancy: 15 % / Biso Wilson estimate: 25.94 Å2 / CC1/2: 0.9 / Net I/σ(I): 6.79
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.686 / Num. unique obs: 20464 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2398refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.1→38.583 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 10224 5 %
Rwork0.2056 194244 -
obs0.208 204468 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.73 Å2 / Biso mean: 27.9909 Å2 / Biso min: 11.97 Å2
Refinement stepCycle: final / Resolution: 2.1→38.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27298 0 466 1572 29336
Biso mean--36.93 30.55 -
Num. residues----3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228144
X-RAY DIFFRACTIONf_angle_d0.61337846
X-RAY DIFFRACTIONf_chiral_restr0.0444353
X-RAY DIFFRACTIONf_plane_restr0.0044824
X-RAY DIFFRACTIONf_dihedral_angle_d14.18417155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14103X-RAY DIFFRACTION5.655TORSIONAL
12B14103X-RAY DIFFRACTION5.655TORSIONAL
13C14103X-RAY DIFFRACTION5.655TORSIONAL
14D14103X-RAY DIFFRACTION5.655TORSIONAL
15E14103X-RAY DIFFRACTION5.655TORSIONAL
16F14103X-RAY DIFFRACTION5.655TORSIONAL
17G14103X-RAY DIFFRACTION5.655TORSIONAL
18H14103X-RAY DIFFRACTION5.655TORSIONAL
19I14103X-RAY DIFFRACTION5.655TORSIONAL
110J14103X-RAY DIFFRACTION5.655TORSIONAL
111K14103X-RAY DIFFRACTION5.655TORSIONAL
112L14103X-RAY DIFFRACTION5.655TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12390.31153410.26496494100
2.1239-2.14890.32993380.25836417100
2.1489-2.17510.31383440.25926530100
2.1751-2.20260.28383390.25086438100
2.2026-2.23160.30843410.27146490100
2.2316-2.26210.36893380.3075641899
2.2621-2.29450.31223400.25326459100
2.2945-2.32870.27493400.23856453100
2.3287-2.36510.29973440.23646531100
2.3651-2.40380.28323380.23466435100
2.4038-2.44530.30743410.23396463100
2.4453-2.48970.27053400.2326470100
2.4897-2.53760.28333440.22756534100
2.5376-2.58940.2833420.2166488100
2.5894-2.64570.28313390.22176445100
2.6457-2.70720.28693410.22486485100
2.7072-2.77490.26713410.21576477100
2.7749-2.84990.27573420.21776491100
2.8499-2.93380.2783400.21736474100
2.9338-3.02840.26353420.20796487100
3.0284-3.13660.25193410.20326484100
3.1366-3.26210.25793410.2126486100
3.2621-3.41050.25043410.2026477100
3.4105-3.59020.23743410.1984646799
3.5902-3.81490.24143400.1883645899
3.8149-4.10920.21293400.1769646999
4.1092-4.52220.20873390.1642643999
4.5222-5.17520.20573430.16436520100
5.1752-6.51510.21463420.18816484100
6.5151-9.390.18843410.1653648198

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