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- PDB-7km1: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant w... -

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Basic information

Entry
Database: PDB / ID: 7km1
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / 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
Chem-3VN / ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME
Authors: Saran, S. / Skovpen, Y. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,28461
Polymers204,9676
Non-polymers5,31755
Water12,376687
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,26924
Polymers68,3222
Non-polymers1,94622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-11 kcal/mol
Surface area21990 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,99919
Polymers68,3222
Non-polymers1,67717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-8 kcal/mol
Surface area22580 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,01618
Polymers68,3222
Non-polymers1,69416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-6 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.010, 230.450, 200.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3:24 or resid 26:28 or resid...
21(chain B and (resid 3:24 or resid 26:28 or resid...
31(chain C and (resid 3:24 or resid 26:28 or resid...
41(chain D and (resid 3:24 or resid 26:28 or resid...
51(chain E and (resid 3:24 or resid 26:28 or resid...
61(chain F and (resid 3:24 or resid 26:28 or resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLU(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 2415 - 36
12SERSERALAALA(chain A and (resid 3:24 or resid 26:28 or resid...AA26 - 2838 - 40
13LEULEUILEILE(chain A and (resid 3:24 or resid 26:28 or resid...AA30 - 3142 - 43
14ARGARGILEILE(chain A and (resid 3:24 or resid 26:28 or resid...AA33 - 3545 - 47
15ASNASNASNASN(chain A and (resid 3:24 or resid 26:28 or resid...AA37 - 5949 - 71
16THRTHRVALVAL(chain A and (resid 3:24 or resid 26:28 or resid...AA61 - 6773 - 79
17THRTHRTHRTHR(chain A and (resid 3:24 or resid 26:28 or resid...AA69 - 7381 - 85
18VALVALASNASN(chain A and (resid 3:24 or resid 26:28 or resid...AA75 - 11287 - 124
19PROPROGLYGLY(chain A and (resid 3:24 or resid 26:28 or resid...AA114 - 141126 - 153
110THRTHRCYSCYS(chain A and (resid 3:24 or resid 26:28 or resid...AA143 - 159155 - 171
111ILEILEVALVAL(chain A and (resid 3:24 or resid 26:28 or resid...AA162 - 165174 - 177
112GLUGLUGLUGLU(chain A and (resid 3:24 or resid 26:28 or resid...AA167 - 228179 - 240
113TYRTYRTYRTYR(chain A and (resid 3:24 or resid 26:28 or resid...AA230242
114LEULEUILEILE(chain A and (resid 3:24 or resid 26:28 or resid...AA240 - 266252 - 278
115SERSERLYSLYS(chain A and (resid 3:24 or resid 26:28 or resid...AA268 - 280280 - 292
116ASNASNMETMET(chain A and (resid 3:24 or resid 26:28 or resid...AA282 - 290294 - 302
117TYRTYRTYRTYR(chain A and (resid 3:24 or resid 26:28 or resid...AA293305
118ILEILEGLYGLY(chain A and (resid 3:24 or resid 26:28 or resid...AA295 - 297307 - 309
119PHEPHEPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA298310
120LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
121LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
122LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
123LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
124LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
125LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
126LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
127LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
128LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
129LYSLYSPHEPHE(chain A and (resid 3:24 or resid 26:28 or resid...AA3 - 29815 - 310
21LYSLYSGLUGLU(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 2415 - 36
22SERSERALAALA(chain B and (resid 3:24 or resid 26:28 or resid...BB26 - 2838 - 40
23LEULEUILEILE(chain B and (resid 3:24 or resid 26:28 or resid...BB30 - 3142 - 43
24ARGARGILEILE(chain B and (resid 3:24 or resid 26:28 or resid...BB33 - 3545 - 47
25ASNASNASNASN(chain B and (resid 3:24 or resid 26:28 or resid...BB37 - 5949 - 71
26THRTHRVALVAL(chain B and (resid 3:24 or resid 26:28 or resid...BB61 - 6773 - 79
27THRTHRTHRTHR(chain B and (resid 3:24 or resid 26:28 or resid...BB69 - 7381 - 85
28VALVALASNASN(chain B and (resid 3:24 or resid 26:28 or resid...BB75 - 11287 - 124
29PROPROGLYGLY(chain B and (resid 3:24 or resid 26:28 or resid...BB114 - 141126 - 153
210THRTHRCYSCYS(chain B and (resid 3:24 or resid 26:28 or resid...BB143 - 159155 - 171
211ILEILEVALVAL(chain B and (resid 3:24 or resid 26:28 or resid...BB162 - 165174 - 177
212GLUGLUGLUGLU(chain B and (resid 3:24 or resid 26:28 or resid...BB167 - 228179 - 240
213TYRTYRTYRTYR(chain B and (resid 3:24 or resid 26:28 or resid...BB230242
214LEULEUILEILE(chain B and (resid 3:24 or resid 26:28 or resid...BB240 - 266252 - 278
215SERSERLYSLYS(chain B and (resid 3:24 or resid 26:28 or resid...BB268 - 280280 - 292
216ASNASNMETMET(chain B and (resid 3:24 or resid 26:28 or resid...BB282 - 290294 - 302
217TYRTYRTYRTYR(chain B and (resid 3:24 or resid 26:28 or resid...BB293305
218ILEILEGLYGLY(chain B and (resid 3:24 or resid 26:28 or resid...BB295 - 297307 - 309
219PHEPHEPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB298310
220LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
221LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
222LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
223LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
224LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
225LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
226LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
227LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
228LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
229LYSLYSPHEPHE(chain B and (resid 3:24 or resid 26:28 or resid...BB3 - 29815 - 310
31LYSLYSGLUGLU(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 2415 - 36
32SERSERALAALA(chain C and (resid 3:24 or resid 26:28 or resid...CC26 - 2838 - 40
33LEULEUILEILE(chain C and (resid 3:24 or resid 26:28 or resid...CC30 - 3142 - 43
34ARGARGILEILE(chain C and (resid 3:24 or resid 26:28 or resid...CC33 - 3545 - 47
35ASNASNASNASN(chain C and (resid 3:24 or resid 26:28 or resid...CC37 - 5949 - 71
36THRTHRVALVAL(chain C and (resid 3:24 or resid 26:28 or resid...CC61 - 6773 - 79
37THRTHRTHRTHR(chain C and (resid 3:24 or resid 26:28 or resid...CC69 - 7381 - 85
38VALVALASNASN(chain C and (resid 3:24 or resid 26:28 or resid...CC75 - 11287 - 124
39PROPROGLYGLY(chain C and (resid 3:24 or resid 26:28 or resid...CC114 - 141126 - 153
310THRTHRCYSCYS(chain C and (resid 3:24 or resid 26:28 or resid...CC143 - 159155 - 171
311ILEILEVALVAL(chain C and (resid 3:24 or resid 26:28 or resid...CC162 - 165174 - 177
312GLUGLUGLUGLU(chain C and (resid 3:24 or resid 26:28 or resid...CC167 - 228179 - 240
313TYRTYRTYRTYR(chain C and (resid 3:24 or resid 26:28 or resid...CC230242
314LEULEUILEILE(chain C and (resid 3:24 or resid 26:28 or resid...CC240 - 266252 - 278
315SERSERLYSLYS(chain C and (resid 3:24 or resid 26:28 or resid...CC268 - 280280 - 292
316ASNASNMETMET(chain C and (resid 3:24 or resid 26:28 or resid...CC282 - 290294 - 302
317TYRTYRTYRTYR(chain C and (resid 3:24 or resid 26:28 or resid...CC293305
318ILEILEGLYGLY(chain C and (resid 3:24 or resid 26:28 or resid...CC295 - 297307 - 309
319PHEPHEPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC298310
320LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
321LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
322LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
323LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
324LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
325LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
326LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
327LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
328LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
329LYSLYSPHEPHE(chain C and (resid 3:24 or resid 26:28 or resid...CC3 - 29815 - 310
41LYSLYSGLUGLU(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 2415 - 36
42SERSERALAALA(chain D and (resid 3:24 or resid 26:28 or resid...DD26 - 2838 - 40
43LEULEUILEILE(chain D and (resid 3:24 or resid 26:28 or resid...DD30 - 3142 - 43
44ARGARGILEILE(chain D and (resid 3:24 or resid 26:28 or resid...DD33 - 3545 - 47
45ASNASNASNASN(chain D and (resid 3:24 or resid 26:28 or resid...DD37 - 5949 - 71
46THRTHRVALVAL(chain D and (resid 3:24 or resid 26:28 or resid...DD61 - 6773 - 79
47THRTHRTHRTHR(chain D and (resid 3:24 or resid 26:28 or resid...DD69 - 7381 - 85
48VALVALASNASN(chain D and (resid 3:24 or resid 26:28 or resid...DD75 - 11287 - 124
49PROPROGLYGLY(chain D and (resid 3:24 or resid 26:28 or resid...DD114 - 141126 - 153
410THRTHRCYSCYS(chain D and (resid 3:24 or resid 26:28 or resid...DD143 - 159155 - 171
411ILEILEVALVAL(chain D and (resid 3:24 or resid 26:28 or resid...DD162 - 165174 - 177
412GLUGLUGLUGLU(chain D and (resid 3:24 or resid 26:28 or resid...DD167 - 228179 - 240
413TYRTYRTYRTYR(chain D and (resid 3:24 or resid 26:28 or resid...DD230242
414LEULEUILEILE(chain D and (resid 3:24 or resid 26:28 or resid...DD240 - 266252 - 278
415SERSERLYSLYS(chain D and (resid 3:24 or resid 26:28 or resid...DD268 - 280280 - 292
416ASNASNMETMET(chain D and (resid 3:24 or resid 26:28 or resid...DD282 - 290294 - 302
417TYRTYRTYRTYR(chain D and (resid 3:24 or resid 26:28 or resid...DD293305
418ILEILEGLYGLY(chain D and (resid 3:24 or resid 26:28 or resid...DD295 - 297307 - 309
419PHEPHEPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD298310
420LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
421LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
422LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
423LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
424LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
425LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
426LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
427LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
428LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
429LYSLYSPHEPHE(chain D and (resid 3:24 or resid 26:28 or resid...DD3 - 29815 - 310
51LYSLYSGLUGLU(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 2415 - 36
52SERSERALAALA(chain E and (resid 3:24 or resid 26:28 or resid...EE26 - 2838 - 40
53LEULEUILEILE(chain E and (resid 3:24 or resid 26:28 or resid...EE30 - 3142 - 43
54ARGARGILEILE(chain E and (resid 3:24 or resid 26:28 or resid...EE33 - 3545 - 47
55ASNASNASNASN(chain E and (resid 3:24 or resid 26:28 or resid...EE37 - 5949 - 71
56THRTHRVALVAL(chain E and (resid 3:24 or resid 26:28 or resid...EE61 - 6773 - 79
57THRTHRTHRTHR(chain E and (resid 3:24 or resid 26:28 or resid...EE69 - 7381 - 85
58VALVALASNASN(chain E and (resid 3:24 or resid 26:28 or resid...EE75 - 11287 - 124
59PROPROGLYGLY(chain E and (resid 3:24 or resid 26:28 or resid...EE114 - 141126 - 153
510THRTHRCYSCYS(chain E and (resid 3:24 or resid 26:28 or resid...EE143 - 159155 - 171
511ILEILEVALVAL(chain E and (resid 3:24 or resid 26:28 or resid...EE162 - 165174 - 177
512GLUGLUGLUGLU(chain E and (resid 3:24 or resid 26:28 or resid...EE167 - 228179 - 240
513TYRTYRTYRTYR(chain E and (resid 3:24 or resid 26:28 or resid...EE230242
514LEULEUILEILE(chain E and (resid 3:24 or resid 26:28 or resid...EE240 - 266252 - 278
515SERSERLYSLYS(chain E and (resid 3:24 or resid 26:28 or resid...EE268 - 280280 - 292
516ASNASNMETMET(chain E and (resid 3:24 or resid 26:28 or resid...EE282 - 290294 - 302
517TYRTYRTYRTYR(chain E and (resid 3:24 or resid 26:28 or resid...EE293305
518ILEILEGLYGLY(chain E and (resid 3:24 or resid 26:28 or resid...EE295 - 297307 - 309
519PHEPHEPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE298310
520LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
521LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
522LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
523LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
524LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
525LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
526LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
527LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
528LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
529LYSLYSPHEPHE(chain E and (resid 3:24 or resid 26:28 or resid...EE3 - 29815 - 310
61LYSLYSGLUGLU(chain F and (resid 3:24 or resid 26:28 or resid...FF3 - 2415 - 36
62SERSERALAALA(chain F and (resid 3:24 or resid 26:28 or resid...FF26 - 2838 - 40
63LEULEUILEILE(chain F and (resid 3:24 or resid 26:28 or resid...FF30 - 3142 - 43
64ARGARGILEILE(chain F and (resid 3:24 or resid 26:28 or resid...FF33 - 3545 - 47
65THRTHRVALVAL(chain F and (resid 3:24 or resid 26:28 or resid...FF61 - 6773 - 79
66THRTHRTHRTHR(chain F and (resid 3:24 or resid 26:28 or resid...FF69 - 7381 - 85
67ASPASPPHEPHE(chain F and (resid 3:24 or resid 26:28 or resid...FF2 - 29814 - 310
68ASPASPPHEPHE(chain F and (resid 3:24 or resid 26:28 or resid...FF2 - 29814 - 310
69ILEILEVALVAL(chain F and (resid 3:24 or resid 26:28 or resid...FF162 - 165174 - 177
610GLUGLUGLUGLU(chain F and (resid 3:24 or resid 26:28 or resid...FF167 - 228179 - 240
611TYRTYRTYRTYR(chain F and (resid 3:24 or resid 26:28 or resid...FF230242
612ILEILEASPASP(chain F and (resid 3:24 or resid 26:28 or resid...FF236 - 238248 - 250
613ASNASNARGARG(chain F and (resid 3:24 or resid 26:28 or resid...FF282 - 29294 - 41
614TYRTYRTYRTYR(chain F and (resid 3:24 or resid 26:28 or resid...FF293305
615ILEILEPHEPHE(chain F and (resid 3:24 or resid 26:28 or resid...FF295 - 298307 - 310

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34161.215 Da / Num. of mol.: 6 / Mutation: H59N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 9 types, 742 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 M Magnesium acetate, 8 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 120 mM R,R-bisLysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2017
RadiationMonochromator: double beam monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→49.556 Å / Num. obs: 167633 / % possible obs: 98.6 % / Redundancy: 15 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.24
Reflection shellResolution: 1.84→1.906 Å / Rmerge(I) obs: 0.5438 / Num. unique obs: 16793 / % possible all: 99.79

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2398refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.84→49.556 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 8381 5 %
Rwork0.1812 159235 -
obs0.1827 167616 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.49 Å2 / Biso mean: 33.0972 Å2 / Biso min: 17.35 Å2
Refinement stepCycle: final / Resolution: 1.84→49.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13675 0 350 687 14712
Biso mean--45.02 36.28 -
Num. residues----1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514215
X-RAY DIFFRACTIONf_angle_d0.90319106
X-RAY DIFFRACTIONf_chiral_restr0.0522187
X-RAY DIFFRACTIONf_plane_restr0.0062431
X-RAY DIFFRACTIONf_dihedral_angle_d15.5698655
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7429X-RAY DIFFRACTION5.452TORSIONAL
12B7429X-RAY DIFFRACTION5.452TORSIONAL
13C7429X-RAY DIFFRACTION5.452TORSIONAL
14D7429X-RAY DIFFRACTION5.452TORSIONAL
15E7429X-RAY DIFFRACTION5.452TORSIONAL
16F7429X-RAY DIFFRACTION5.452TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.84-1.86090.33162820.29045351100
1.8609-1.88280.34732790.28595302100
1.8828-1.90580.29512790.25115299100
1.9058-1.92990.29152810.24095348100
1.9299-1.95530.27132780.23615279100
1.9553-1.98210.27092830.22135370100
1.9821-2.01040.26182790.21835308100
2.0104-2.04040.26812800.21615308100
2.0404-2.07230.25032780.2177531199
2.0723-2.10630.24412760.2126523598
2.1063-2.14260.23792810.19295334100
2.1426-2.18150.23782810.19295355100
2.1815-2.22350.21362790.1872529299
2.2235-2.26890.22392800.1823532399
2.2689-2.31820.21532810.182534199
2.3182-2.37210.24082780.1873527799
2.3721-2.43150.23112780.1904527799
2.4315-2.49720.2292810.1819533999
2.4972-2.57070.21972750.1742523398
2.5707-2.65370.21382790.1724529699
2.6537-2.74850.21392790.1732530799
2.7485-2.85850.19692800.1784531999
2.8585-2.98860.25462750.1808522197
2.9886-3.14610.20412780.1748527597
3.1461-3.34320.19442730.1822520297
3.3432-3.60130.19252770.1773525397
3.6013-3.96360.18952800.1694532398
3.9636-4.53680.1722760.1586524596
4.5368-5.71450.18482830.1727537598
5.7145-8.230.1982920.1644553797

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