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- PDB-6tzu: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant w... -

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Basic information

Entry
Database: PDB / ID: 6tzu
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site
Components(4-hydroxy-tetrahydrodipicolinate ...) x 2
KeywordsLYASE / Dihydrodipicolinate synthase / Campylobacter jejuni / Tetrameric protein / TIM barrel / Allostery
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
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Lehnert, C. / 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_conn_type / 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.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_conn_type.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 1.3Nov 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)208,27361
Polymers204,5086
Non-polymers3,76555
Water23,7981321
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,74339
Polymers136,3624
Non-polymers2,38235
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-21 kcal/mol
Surface area40590 Å2
MethodPISA
2
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)139,06044
Polymers136,2934
Non-polymers2,76740
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area16710 Å2
ΔGint-13 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.930, 225.810, 200.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11F-458-

HOH

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
13SERSERILEILE(chain A and (resid 3:20 or resid 22:24 or resid...AA26 - 3138 - 43
14ARGARGTHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA33 - 5545 - 67
15THRTHRTHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA6981
16THRTHRVALVAL(chain A and (resid 3:20 or resid 22:24 or resid...AA61 - 6773 - 79
17ILEILETHRTHR(chain A and (resid 3:20 or resid 22:24 or resid...AA65 - 7377 - 85
18LYSLYSLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA76 - 9488 - 106
19HISHISLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA99 - 97111 - 109
110LYSLYSPHEPHE(chain A and (resid 3:20 or resid 22:24 or resid...AA3 - 29815 - 310
111LYSLYSPHEPHE(chain A and (resid 3:20 or resid 22:24 or resid...AA3 - 29815 - 310
112ASNASNVALVAL(chain A and (resid 3:20 or resid 22:24 or resid...AA161 - 165173 - 177
113ALAALAASPASP(chain A and (resid 3:20 or resid 22:24 or resid...AA220 - 238232 - 250
114ALAALALYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA220 - 231232 - 243
115ALAALALYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA233 - 234245 - 246
116ILEILEILEILE(chain A and (resid 3:20 or resid 22:24 or resid...AA236 - 266248 - 278
117ASNASNVALVAL(chain A and (resid 3:20 or resid 22:24 or resid...AA282 - 289294 - 301
118VALVALLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA289 - 296301 - 308
119VALVALLYSLYS(chain A and (resid 3:20 or resid 22:24 or resid...AA289 - 291301 - 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
23SERSERILEILE(chain B and (resid 3:20 or resid 22:24 or resid...BB26 - 3138 - 43
24ARGARGTHRTHR(chain B and (resid 3:20 or resid 22:24 or resid...BB33 - 5545 - 67
25THRTHRTHRTHR(chain B and (resid 3:20 or resid 22:24 or resid...BB6981
26THRTHRVALVAL(chain B and (resid 3:20 or resid 22:24 or resid...BB61 - 6773 - 79
27ILEILETHRTHR(chain B and (resid 3:20 or resid 22:24 or resid...BB65 - 7377 - 85
28LYSLYSLYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB76 - 9488 - 106
29HISHISLYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB99 - 97111 - 109
210HISHISPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB-5 - 2987 - 310
211HISHISPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB-5 - 2987 - 310
212ASNASNVALVAL(chain B and (resid 3:20 or resid 22:24 or resid...BB161 - 165173 - 177
213ALAALAASPASP(chain B and (resid 3:20 or resid 22:24 or resid...BB220 - 238232 - 250
214ALAALALYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB220 - 231232 - 243
215ALAALALYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB233 - 234245 - 246
216ILEILEILEILE(chain B and (resid 3:20 or resid 22:24 or resid...BB236 - 266248 - 278
217ASNASNVALVAL(chain B and (resid 3:20 or resid 22:24 or resid...BB282 - 289294 - 301
218VALVALLYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB289 - 296301 - 308
219VALVALLYSLYS(chain B and (resid 3:20 or resid 22:24 or resid...BB289 - 291301 - 303
220TYRTYRTYRTYR(chain B and (resid 3:20 or resid 22:24 or resid...BB293305
221ILEILEPHEPHE(chain B and (resid 3:20 or resid 22:24 or resid...BB295 - 298307 - 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
33SERSERILEILE(chain C and (resid 3:20 or resid 22:24 or resid...CC26 - 3138 - 43
34ARGARGTHRTHR(chain C and (resid 3:20 or resid 22:24 or resid...CC33 - 5545 - 67
35THRTHRTHRTHR(chain C and (resid 3:20 or resid 22:24 or resid...CC6981
36THRTHRVALVAL(chain C and (resid 3:20 or resid 22:24 or resid...CC61 - 6773 - 79
37ILEILETHRTHR(chain C and (resid 3:20 or resid 22:24 or resid...CC65 - 7377 - 85
38LYSLYSLYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC76 - 9488 - 106
39HISHISLYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC99 - 97111 - 109
310LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
311LYSLYSPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC3 - 29815 - 310
312ASNASNVALVAL(chain C and (resid 3:20 or resid 22:24 or resid...CC161 - 165173 - 177
313ALAALAASPASP(chain C and (resid 3:20 or resid 22:24 or resid...CC220 - 238232 - 250
314ALAALALYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC220 - 231232 - 243
315ALAALALYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC233 - 234245 - 246
316ILEILEILEILE(chain C and (resid 3:20 or resid 22:24 or resid...CC236 - 266248 - 278
317ASNASNVALVAL(chain C and (resid 3:20 or resid 22:24 or resid...CC282 - 289294 - 301
318VALVALLYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC289 - 296301 - 308
319VALVALLYSLYS(chain C and (resid 3:20 or resid 22:24 or resid...CC289 - 291301 - 303
320TYRTYRTYRTYR(chain C and (resid 3:20 or resid 22:24 or resid...CC293305
321ILEILEPHEPHE(chain C and (resid 3:20 or resid 22:24 or resid...CC295 - 298307 - 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
43SERSERILEILE(chain D and (resid 3:20 or resid 22:24 or resid...DD26 - 3138 - 43
44ARGARGTHRTHR(chain D and (resid 3:20 or resid 22:24 or resid...DD33 - 5545 - 67
45THRTHRTHRTHR(chain D and (resid 3:20 or resid 22:24 or resid...DD6981
46THRTHRVALVAL(chain D and (resid 3:20 or resid 22:24 or resid...DD61 - 6773 - 79
47ILEILETHRTHR(chain D and (resid 3:20 or resid 22:24 or resid...DD65 - 7377 - 85
48LYSLYSLYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD76 - 9488 - 106
49HISHISLYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD99 - 97111 - 109
410HISHISPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD-7 - 2985 - 310
411HISHISPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD-7 - 2985 - 310
412ASNASNVALVAL(chain D and (resid 3:20 or resid 22:24 or resid...DD161 - 165173 - 177
413ALAALAASPASP(chain D and (resid 3:20 or resid 22:24 or resid...DD220 - 238232 - 250
414ALAALALYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD220 - 231232 - 243
415ALAALALYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD233 - 234245 - 246
416ILEILEILEILE(chain D and (resid 3:20 or resid 22:24 or resid...DD236 - 266248 - 278
417ASNASNVALVAL(chain D and (resid 3:20 or resid 22:24 or resid...DD282 - 289294 - 301
418VALVALLYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD289 - 296301 - 308
419VALVALLYSLYS(chain D and (resid 3:20 or resid 22:24 or resid...DD289 - 291301 - 303
420TYRTYRTYRTYR(chain D and (resid 3:20 or resid 22:24 or resid...DD293305
421ILEILEPHEPHE(chain D and (resid 3:20 or resid 22:24 or resid...DD295 - 298307 - 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
53SERSERILEILE(chain E and (resid 3:20 or resid 22:24 or resid...EE26 - 3138 - 43
54ARGARGTHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE33 - 5545 - 67
55THRTHRTHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE6981
56THRTHRVALVAL(chain E and (resid 3:20 or resid 22:24 or resid...EE61 - 6773 - 79
57ILEILETHRTHR(chain E and (resid 3:20 or resid 22:24 or resid...EE65 - 7377 - 85
58LYSLYSLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE76 - 9488 - 106
59HISHISLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE99 - 97111 - 109
510ASPASPPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE2 - 29814 - 310
511ASPASPPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE2 - 29814 - 310
512ASNASNVALVAL(chain E and (resid 3:20 or resid 22:24 or resid...EE161 - 165173 - 177
513ALAALAASPASP(chain E and (resid 3:20 or resid 22:24 or resid...EE220 - 238232 - 250
514ALAALALYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE220 - 231232 - 243
515ALAALALYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE233 - 234245 - 246
516ILEILEILEILE(chain E and (resid 3:20 or resid 22:24 or resid...EE236 - 266248 - 278
517ASNASNVALVAL(chain E and (resid 3:20 or resid 22:24 or resid...EE282 - 289294 - 301
518VALVALLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE289 - 296301 - 308
519VALVALLYSLYS(chain E and (resid 3:20 or resid 22:24 or resid...EE289 - 291301 - 303
520TYRTYRTYRTYR(chain E and (resid 3:20 or resid 22:24 or resid...EE293305
521ILEILEPHEPHE(chain E and (resid 3:20 or resid 22:24 or resid...EE295 - 298307 - 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
63SERSERILEILE(chain F and (resid 3:20 or resid 22:24 or resid...FF26 - 3138 - 43
64ARGARGTHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF33 - 5545 - 67
65THRTHRTHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF6981
66THRTHRVALVAL(chain F and (resid 3:20 or resid 22:24 or resid...FF61 - 6773 - 79
67ILEILETHRTHR(chain F and (resid 3:20 or resid 22:24 or resid...FF65 - 7377 - 85
68LYSLYSLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF76 - 9488 - 106
69HISHISLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF99 - 97111 - 109
610LYSLYSPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF3 - 29815 - 310
611LYSLYSPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF3 - 29815 - 310
612ASNASNVALVAL(chain F and (resid 3:20 or resid 22:24 or resid...FF161 - 165173 - 177
613ALAALAASPASP(chain F and (resid 3:20 or resid 22:24 or resid...FF220 - 238232 - 250
614ALAALALYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF220 - 231232 - 243
615ALAALALYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF233 - 234245 - 246
616ILEILEILEILE(chain F and (resid 3:20 or resid 22:24 or resid...FF236 - 266248 - 278
617ASNASNVALVAL(chain F and (resid 3:20 or resid 22:24 or resid...FF282 - 289294 - 301
618VALVALLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF289 - 296301 - 308
619VALVALLYSLYS(chain F and (resid 3:20 or resid 22:24 or resid...FF289 - 291301 - 303
620TYRTYRTYRTYR(chain F and (resid 3:20 or resid 22:24 or resid...FF293305
621ILEILEPHEPHE(chain F and (resid 3:20 or resid 22:24 or resid...FF295 - 298307 - 310

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Components

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4-hydroxy-tetrahydrodipicolinate ... , 2 types, 6 molecules ABCDEF

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


Mass: 34073.195 Da / Num. of mol.: 5 / Mutation: N84A
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
#2: Protein 4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34142.234 Da / Num. of mol.: 1 / Mutation: N84A
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 , 7 types, 1376 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / 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: 2.32 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.1 M Magnesium acetate, 12 % 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: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→49.204 Å / Num. obs: 177638 / % possible obs: 100 % / Redundancy: 7.107 % / Biso Wilson estimate: 21.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.123 / Χ2: 1.037 / Net I/σ(I): 12.71 / Num. measured all: 1262447 / Scaling rejects: 193
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
1.8-1.917.1420.8192.2620489328691286890.7960.883100
1.91-2.037.2140.5043.817790024661246600.9160.543100
2.03-2.177.2330.3166.1116157622341223400.9620.341100
2.17-2.347.2290.2228.7314778220444204440.980.239100
2.34-2.537.2260.17410.9112171016847168440.9880.188100
2.53-2.757.1740.12614.7910169214183141750.9930.13699.9
2.75-3.027.1070.09818.328677812217122100.9960.10599.9
3.02-3.356.9530.07323.827032510119101140.9970.079100
3.35-3.776.7970.05528.9956343829682890.9980.05999.9
3.77-4.36.7260.04533.3442917638963810.9980.04999.9
4.3-56.7480.04234.4732588484048290.9990.04699.8
5-49.2046.6890.03635.3457943869386630.9990.03999.7

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Processing

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

4ly8


Resolution: 1.8→49.204 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.23
RfactorNum. reflection% reflection
Rfree0.2014 8881 5 %
Rwork0.1725 --
obs0.1739 177619 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.99 Å2 / Biso mean: 22.479 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.8→49.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13797 0 245 1321 15363
Biso mean--38.5 29.05 -
Num. residues----1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414270
X-RAY DIFFRACTIONf_angle_d0.76819196
X-RAY DIFFRACTIONf_chiral_restr0.052196
X-RAY DIFFRACTIONf_plane_restr0.0052458
X-RAY DIFFRACTIONf_dihedral_angle_d14.9348667
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7287X-RAY DIFFRACTION4.635TORSIONAL
12B7287X-RAY DIFFRACTION4.635TORSIONAL
13C7287X-RAY DIFFRACTION4.635TORSIONAL
14D7287X-RAY DIFFRACTION4.635TORSIONAL
15E7287X-RAY DIFFRACTION4.635TORSIONAL
16F7287X-RAY DIFFRACTION4.635TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.82050.35852900.31915513
1.8205-1.84190.29362950.2785598
1.8419-1.86430.27242940.23755584
1.8643-1.88790.2672950.23635608
1.8879-1.91280.26752920.21795560
1.9128-1.9390.24862940.20025579
1.939-1.96670.23512940.25576
1.9667-1.9960.22772920.18835575
1.996-2.02720.21972950.18295607
2.0272-2.06050.22972940.19155569
2.0605-2.0960.23532940.18875594
2.096-2.13410.23342960.18695616
2.1341-2.17520.21052940.1725599
2.1752-2.21960.21712930.16555563
2.2196-2.26780.20752970.16345638
2.2678-2.32060.1992950.165614
2.3206-2.37860.18632940.15915585
2.3786-2.44290.21772960.17125614
2.4429-2.51480.19992970.1685642
2.5148-2.5960.19412930.16095583
2.596-2.68870.19412980.16165646
2.6887-2.79640.19612970.16385643
2.7964-2.92360.22442950.17655618
2.9236-3.07780.20222960.17615627
3.0778-3.27060.21112990.18085678
3.2706-3.5230.20882980.17885653
3.523-3.87740.16172990.15295693
3.8774-4.43820.16193000.14065682
4.4382-5.59040.15373030.14835759
5.59040.18553120.17115922

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