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- PDB-6u01: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant w... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6u01
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase / TIM barrel / Tetrameric protein
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Lehnert, L. / Palmer, D.R.J. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.
Authors: Majdi Yazdi, M. / Saran, S. / Mrozowich, T. / Lehnert, C. / Patel, T.R. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 1.3Nov 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)207,29336
Polymers205,1176
Non-polymers2,17630
Water17,781987
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,09322
Polymers136,7454
Non-polymers1,34818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-51 kcal/mol
Surface area39840 Å2
MethodPISA
2
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,40228
Polymers136,7454
Non-polymers1,65724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area14040 Å2
ΔGint-24 kcal/mol
Surface area39950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.990, 231.420, 200.650
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 3:20 or resid 22:24 or resid...
21(chain B and (resid 3:20 or resid 22:24 or resid...
31(chain C and (resid 3:20 or resid 22:24 or resid...
41(chain D and (resid 3:20 or resid 22:24 or resid...
51(chain E and (resid 3:20 or resid 22:24 or resid...
61(chain F and (resid 3:20 or resid 22:24 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
11LYSLYSGLYGLY(chain A and (resid 3:20 or resid 22:24 or resid...AA3 - 2015 - 32
12VALVALGLUGLU(chain A and (resid 3:20 or resid 22:24 or resid...AA22 - 2434 - 36
13SERSERALAALA(chain A and (resid 3:20 or resid 22:24 or resid...AA26 - 2838 - 40
14LEULEUILEILE(chain A and (resid 3:20 or resid 22:24 or resid...AA30 - 3142 - 43
15THRTHRTHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA61 - 5573 - 67
16GLUGLUGLUGLU(chain A and (resid 3:20 or resid 22:24 or resid...AA5870
17ILEILETHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA65 - 7377 - 85
18LEULEUTHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA78 - 8690 - 98
19THRTHRLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA86 - 9498 - 106
110HISHISLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA99 - 97111 - 109
111LYSLYSPHEPHE(chain A and (resid 3:20 or resid 22:24 or resid...AA3 - 29815 - 310
112LYSLYSPHEPHE(chain A and (resid 3:20 or resid 22:24 or resid...AA3 - 29815 - 310
113GLUGLUPROPRO(chain A and (resid 3:20 or resid 22:24 or resid...AA167 - 183179 - 195
114TYRTYRTYRTYR(chain A and (resid 3:20 or resid 22:24 or resid...AA230242
115TYRTYRTYRTYR(chain A and (resid 3:20 or resid 22:24 or resid...AA230242
116ALAALALYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA233 - 234245 - 246
117ILEILEILEILE(chain A and (resid 3:20 or resid 22:24 or resid...AA236 - 266248 - 278
118ASNASNLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA282 - 291294 - 303
119ASNASNLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA282 - 291294 - 303
120TYRTYRTYRTYR(chain A and (resid 3:20 or resid 22:24 or resid...AA293305
121ILEILEPHEPHE(chain A and (resid 3:20 or resid 22:24 or resid...AA295 - 298307 - 310
21LYSLYSGLYGLY(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 2015 - 32
22VALVALGLUGLU(chain B and (resid 3:20 or resid 22:24 or resid...BB22 - 2434 - 36
23SERSERALAALA(chain B and (resid 3:20 or resid 22:24 or resid...BB26 - 2838 - 40
24LEULEUILEILE(chain B and (resid 3:20 or resid 22:24 or resid...BB30 - 3142 - 43
25GLUGLUGLUGLU(chain B and (resid 3:20 or resid 22:24 or resid...BB5870
26VALVALTHRTHR(chain B and (resid 3:20 or resid 22:24 or resid...BB75 - 7387 - 85
27GLUGLUTHRTHR(chain B and (resid 3:20 or resid 22:24 or resid...BB88 - 86100 - 98
28ALAALALYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB96 - 94108 - 106
29LYSLYSLYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 9715 - 109
210LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
211GLUGLUCYSCYS(chain B and (resid 3:20 or resid 22:24 or resid...BB146 - 159158 - 171
212ILEILEVALVAL(chain B and (resid 3:20 or resid 22:24 or resid...BB162 - 165174 - 177
213GLUGLUPROPRO(chain B and (resid 3:20 or resid 22:24 or resid...BB167 - 183179 - 195
214METMETILEILE(chain B and (resid 3:20 or resid 22:24 or resid...BB185 - 218197 - 230
215ALAALAGLUGLU(chain B and (resid 3:20 or resid 22:24 or resid...BB220 - 228232 - 240
216ILEILEILEILE(chain B and (resid 3:20 or resid 22:24 or resid...BB236 - 266248 - 278
217LEULEUSERSER(chain B and (resid 3:20 or resid 22:24 or resid...BB269 - 277281 - 289
218PROPROPROPRO(chain B and (resid 3:20 or resid 22:24 or resid...BB278290
219LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
220LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
221LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
222LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
223LYSLYSPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB3 - 29815 - 310
31LYSLYSGLYGLY(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 2015 - 32
32VALVALGLUGLU(chain C and (resid 3:20 or resid 22:24 or resid...CC22 - 2434 - 36
33SERSERALAALA(chain C and (resid 3:20 or resid 22:24 or resid...CC26 - 2838 - 40
34LEULEUILEILE(chain C and (resid 3:20 or resid 22:24 or resid...CC30 - 3142 - 43
35GLUGLUGLUGLU(chain C and (resid 3:20 or resid 22:24 or resid...CC5870
36VALVALTHRTHR(chain C and (resid 3:20 or resid 22:24 or resid...CC75 - 7387 - 85
37GLUGLUTHRTHR(chain C and (resid 3:20 or resid 22:24 or resid...CC88 - 86100 - 98
38ALAALALYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC96 - 94108 - 106
39LYSLYSLYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 9715 - 109
310LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
311GLUGLUCYSCYS(chain C and (resid 3:20 or resid 22:24 or resid...CC146 - 159158 - 171
312ILEILEVALVAL(chain C and (resid 3:20 or resid 22:24 or resid...CC162 - 165174 - 177
313GLUGLUPROPRO(chain C and (resid 3:20 or resid 22:24 or resid...CC167 - 183179 - 195
314METMETILEILE(chain C and (resid 3:20 or resid 22:24 or resid...CC185 - 218197 - 230
315ALAALAGLUGLU(chain C and (resid 3:20 or resid 22:24 or resid...CC220 - 228232 - 240
316ILEILEILEILE(chain C and (resid 3:20 or resid 22:24 or resid...CC236 - 266248 - 278
317LEULEUSERSER(chain C and (resid 3:20 or resid 22:24 or resid...CC269 - 277281 - 289
318PROPROPROPRO(chain C and (resid 3:20 or resid 22:24 or resid...CC278290
319LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
320LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
321LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
322LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
323LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
41LYSLYSGLYGLY(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 2015 - 32
42VALVALGLUGLU(chain D and (resid 3:20 or resid 22:24 or resid...DD22 - 2434 - 36
43SERSERALAALA(chain D and (resid 3:20 or resid 22:24 or resid...DD26 - 2838 - 40
44LEULEUILEILE(chain D and (resid 3:20 or resid 22:24 or resid...DD30 - 3142 - 43
45GLUGLUGLUGLU(chain D and (resid 3:20 or resid 22:24 or resid...DD5870
46VALVALTHRTHR(chain D and (resid 3:20 or resid 22:24 or resid...DD75 - 7387 - 85
47GLUGLUTHRTHR(chain D and (resid 3:20 or resid 22:24 or resid...DD88 - 86100 - 98
48ALAALALYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD96 - 94108 - 106
49LYSLYSLYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 9715 - 109
410LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
411GLUGLUCYSCYS(chain D and (resid 3:20 or resid 22:24 or resid...DD146 - 159158 - 171
412ILEILEVALVAL(chain D and (resid 3:20 or resid 22:24 or resid...DD162 - 165174 - 177
413GLUGLUPROPRO(chain D and (resid 3:20 or resid 22:24 or resid...DD167 - 183179 - 195
414METMETILEILE(chain D and (resid 3:20 or resid 22:24 or resid...DD185 - 218197 - 230
415ALAALAGLUGLU(chain D and (resid 3:20 or resid 22:24 or resid...DD220 - 228232 - 240
416ILEILEILEILE(chain D and (resid 3:20 or resid 22:24 or resid...DD236 - 266248 - 278
417LEULEUSERSER(chain D and (resid 3:20 or resid 22:24 or resid...DD269 - 277281 - 289
418PROPROPROPRO(chain D and (resid 3:20 or resid 22:24 or resid...DD278290
419LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
420LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
421LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
422LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
423LYSLYSPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD3 - 29815 - 310
51LYSLYSGLYGLY(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 2015 - 32
52VALVALGLUGLU(chain E and (resid 3:20 or resid 22:24 or resid...EE22 - 2434 - 36
53SERSERALAALA(chain E and (resid 3:20 or resid 22:24 or resid...EE26 - 2838 - 40
54LEULEUILEILE(chain E and (resid 3:20 or resid 22:24 or resid...EE30 - 3142 - 43
55THRTHRTHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE61 - 5573 - 67
56GLUGLUGLUGLU(chain E and (resid 3:20 or resid 22:24 or resid...EE5870
57ILEILETHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE65 - 7377 - 85
58LEULEUTHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE78 - 8690 - 98
59THRTHRLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE86 - 9498 - 106
510HISHISLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE99 - 97111 - 109
511LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
512LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
513GLUGLUPROPRO(chain E and (resid 3:20 or resid 22:24 or resid...EE167 - 183179 - 195
514TYRTYRTYRTYR(chain E and (resid 3:20 or resid 22:24 or resid...EE230242
515TYRTYRTYRTYR(chain E and (resid 3:20 or resid 22:24 or resid...EE230242
516ALAALALYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE233 - 234245 - 246
517ILEILEILEILE(chain E and (resid 3:20 or resid 22:24 or resid...EE236 - 266248 - 278
518PROPROPROPRO(chain E and (resid 3:20 or resid 22:24 or resid...EE278290
519LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
520LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
521LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
522LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
523LYSLYSPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE3 - 29815 - 310
61LYSLYSGLYGLY(chain F and (resid 3:20 or resid 22:24 or resid...FF3 - 2015 - 32
62VALVALGLUGLU(chain F and (resid 3:20 or resid 22:24 or resid...FF22 - 2434 - 36
63SERSERALAALA(chain F and (resid 3:20 or resid 22:24 or resid...FF26 - 2838 - 40
64LEULEUILEILE(chain F and (resid 3:20 or resid 22:24 or resid...FF30 - 3142 - 43
65THRTHRTHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF61 - 5573 - 67
66GLUGLUGLUGLU(chain F and (resid 3:20 or resid 22:24 or resid...FF5870
67ILEILETHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF65 - 7377 - 85
68LEULEUTHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF78 - 8690 - 98
69THRTHRLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF86 - 9498 - 106
610HISHISLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF99 - 97111 - 109
611ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
612ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
613GLUGLUPROPRO(chain F and (resid 3:20 or resid 22:24 or resid...FF167 - 183179 - 195
614TYRTYRTYRTYR(chain F and (resid 3:20 or resid 22:24 or resid...FF230242
615TYRTYRTYRTYR(chain F and (resid 3:20 or resid 22:24 or resid...FF230242
616ALAALALYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF233 - 234245 - 246
617ILEILEILEILE(chain F and (resid 3:20 or resid 22:24 or resid...FF236 - 266248 - 278
618PROPROPROPRO(chain F and (resid 3:20 or resid 22:24 or resid...FF278290
619ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
620ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
621ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
622ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 310
623ASPASPPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF2 - 29814 - 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: 34186.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: dapA_1, dapA, A6J93_04235, C9J79_06575, DDV78_09110, EBI45_07605, NCTC13362_01713
Production host: Escherichia coli (E. coli)
References: UniProt: A0A2U0QMK8, UniProt: Q9PPB4*PLUS, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 8 types, 1017 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.7 M Magnesium acetate, 10 % PEG8000 0.1 M Sodium acetate (pH 7.4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→43.436 Å / Num. obs: 161269 / % possible obs: 99.2 % / Redundancy: 3.437 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.112 / Χ2: 0.975 / Net I/σ(I): 7.85 / Num. measured all: 554299 / Scaling rejects: 205
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.87-1.923.5050.5672.064173811916119090.7420.6799.9
1.92-1.973.5140.4852.424076211608115990.8050.57399.9
1.97-2.033.5140.3683.23981211346113300.8740.43599.9
2.03-2.093.5140.3053.893850710977109590.9030.3699.8
2.09-2.163.4980.2464.773729610700106610.9340.29199.6
2.16-2.243.4920.215.533591510319102850.9520.24999.7
2.24-2.323.4660.1836.2234255994498840.960.21799.4
2.32-2.413.4640.1577.133201963095850.9710.18699.5
2.41-2.523.4430.1417.7531397919691190.9730.16899.2
2.52-2.643.4080.1199.229898883687730.9780.14299.3
2.64-2.793.3920.10610.1128107838382860.980.12698.8
2.79-2.963.3660.09610.8726363793978310.9840.11498.6
2.96-3.163.3690.08512.0224823751373670.9850.10298.1
3.16-3.413.3410.07913.123000699968850.9850.09498.4
3.41-3.743.330.07214.0520942644462890.9880.08697.6
3.74-4.183.3030.0714.718780582556860.9860.08397.6
4.18-4.833.3580.06515.1817172519551130.9850.07898.4
4.83-5.913.3690.05915.1114726441443710.990.0799
5.91-8.363.3450.0615.3711499346934380.9910.07199.1
8.36-43.4363.2150.05515.576106199418990.9930.06695.2

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Processing

Software
NameVersionClassification
PHENIXdev_2398refinement
Cootmodel building
XSCALE3.25data scaling
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.87→43.436 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 8064 5 %
Rwork0.1894 153190 -
obs0.191 161254 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.83 Å2 / Biso mean: 28.3492 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 1.87→43.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13672 0 140 987 14799
Biso mean--39.59 34.02 -
Num. residues----1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414057
X-RAY DIFFRACTIONf_angle_d0.79818947
X-RAY DIFFRACTIONf_chiral_restr0.0492180
X-RAY DIFFRACTIONf_plane_restr0.0052417
X-RAY DIFFRACTIONf_dihedral_angle_d14.8238572
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7194X-RAY DIFFRACTION4.641TORSIONAL
12B7194X-RAY DIFFRACTION4.641TORSIONAL
13C7194X-RAY DIFFRACTION4.641TORSIONAL
14D7194X-RAY DIFFRACTION4.641TORSIONAL
15E7194X-RAY DIFFRACTION4.641TORSIONAL
16F7194X-RAY DIFFRACTION4.641TORSIONAL
LS refinement shell

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

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-1.89120.3372700.30395122100
1.8912-1.91350.31892670.27845075100
1.9135-1.93680.30392670.2665078100
1.9368-1.96140.29622700.25235121100
1.9614-1.98720.28572680.23715103100
1.9872-2.01440.26692690.22445108100
2.0144-2.04320.25142670.21125060100
2.0432-2.07370.25882690.20645108100
2.0737-2.10610.24692680.20445098100
2.1061-2.14060.27232690.20615110100
2.1406-2.17750.26642690.20585109100
2.1775-2.21710.2322670.20255070100
2.2171-2.25970.25322690.20535120100
2.2597-2.30590.26582670.2015508199
2.3059-2.3560.22972700.1896511599
2.356-2.41080.22992680.19795089100
2.4108-2.47110.24112680.1996509399
2.4711-2.53790.23712670.1898508499
2.5379-2.61250.20192690.1755511599
2.6125-2.69690.21732680.1836507999
2.6969-2.79320.2282670.1879508399
2.7932-2.9050.2472680.2003509399
2.905-3.03720.24222680.1986507998
3.0372-3.19730.22082650.1945505298
3.1973-3.39760.23252690.1949511298
3.3976-3.65980.19932670.1831505697
3.6598-4.02780.18722670.1683508598
4.0278-4.61010.18372700.1579513298
4.6101-5.80610.20252750.1698521099
5.80610.17142820.1731535098

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