[English] 日本語
Yorodumi
- PDB-7kg5: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kg5
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active 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
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: 1.95 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: Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni
Authors: Majdi Yazd, M. / Reddy Annadi, K. / Saran, S. / Bhagwa, A. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)210,23674
Polymers205,4006
Non-polymers4,83668
Water16,952941
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,05023
Polymers68,4672
Non-polymers1,58421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint3 kcal/mol
Surface area22450 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,40429
Polymers68,4672
Non-polymers1,93727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint6 kcal/mol
Surface area22390 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78122
Polymers68,4672
Non-polymers1,31420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-28 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.130, 231.250, 202.100
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3:24 or resid 26:28 or resid...A3 - 24
121(chain A and (resid 3:24 or resid 26:28 or resid...A26 - 28
131(chain A and (resid 3:24 or resid 26:28 or resid...A30 - 31
141(chain A and (resid 3:24 or resid 26:28 or resid...A33 - 50
151(chain A and (resid 3:24 or resid 26:28 or resid...A52 - 55
161(chain A and (resid 3:24 or resid 26:28 or resid...A58 - 59
171(chain A and (resid 3:24 or resid 26:28 or resid...A61 - 67
181(chain A and (resid 3:24 or resid 26:28 or resid...A69 - 73
191(chain A and (resid 3:24 or resid 26:28 or resid...A75 - 86
1101(chain A and (resid 3:24 or resid 26:28 or resid...A88 - 94
1111(chain A and (resid 3:24 or resid 26:28 or resid...A96 - 97
1121(chain A and (resid 3:24 or resid 26:28 or resid...A99 - 149
1131(chain A and (resid 3:24 or resid 26:28 or resid...A151 - 165
1141(chain A and (resid 3:24 or resid 26:28 or resid...A167 - 183
1151(chain A and (resid 3:24 or resid 26:28 or resid...A185 - 218
1161(chain A and (resid 3:24 or resid 26:28 or resid...A220 - 230
1171(chain A and (resid 3:24 or resid 26:28 or resid...A233 - 2379
1181(chain A and (resid 3:24 or resid 26:28 or resid...A281 - 290
1191(chain A and (resid 3:24 or resid 26:28 or resid...A293290
1201(chain A and (resid 3:24 or resid 26:28 or resid...A293
1211(chain A and (resid 3:24 or resid 26:28 or resid...A295 - 297
1221(chain A and (resid 3:24 or resid 26:28 or resid...A298
1231(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1241(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1251(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1261(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1271(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1281(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1291(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1301(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
1311(chain A and (resid 3:24 or resid 26:28 or resid...A2 - 298
211(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 24
221(chain B and (resid 3:24 or resid 26:28 or resid...B26 - 28
231(chain B and (resid 3:24 or resid 26:28 or resid...B30 - 31
241(chain B and (resid 3:24 or resid 26:28 or resid...B33 - 50
251(chain B and (resid 3:24 or resid 26:28 or resid...B52 - 55
261(chain B and (resid 3:24 or resid 26:28 or resid...B58 - 59
271(chain B and (resid 3:24 or resid 26:28 or resid...B61 - 67
281(chain B and (resid 3:24 or resid 26:28 or resid...B69 - 73
291(chain B and (resid 3:24 or resid 26:28 or resid...B75 - 86
2101(chain B and (resid 3:24 or resid 26:28 or resid...B88 - 94
2111(chain B and (resid 3:24 or resid 26:28 or resid...B96 - 97
2121(chain B and (resid 3:24 or resid 26:28 or resid...B99 - 149
2131(chain B and (resid 3:24 or resid 26:28 or resid...B151 - 165
2141(chain B and (resid 3:24 or resid 26:28 or resid...B167 - 183
2151(chain B and (resid 3:24 or resid 26:28 or resid...B185 - 218
2161(chain B and (resid 3:24 or resid 26:28 or resid...B220 - 230
2171(chain B and (resid 3:24 or resid 26:28 or resid...B233 - 2379
2181(chain B and (resid 3:24 or resid 26:28 or resid...B281 - 290
2191(chain B and (resid 3:24 or resid 26:28 or resid...B293290
2201(chain B and (resid 3:24 or resid 26:28 or resid...B293
2211(chain B and (resid 3:24 or resid 26:28 or resid...B295 - 297
2221(chain B and (resid 3:24 or resid 26:28 or resid...B298
2231(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2241(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2251(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2261(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2271(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2281(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2291(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2301(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
2311(chain B and (resid 3:24 or resid 26:28 or resid...B3 - 298
311(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 24
321(chain C and (resid 3:24 or resid 26:28 or resid...C26 - 28
331(chain C and (resid 3:24 or resid 26:28 or resid...C30 - 31
341(chain C and (resid 3:24 or resid 26:28 or resid...C33 - 50
351(chain C and (resid 3:24 or resid 26:28 or resid...C52 - 55
361(chain C and (resid 3:24 or resid 26:28 or resid...C58 - 59
371(chain C and (resid 3:24 or resid 26:28 or resid...C61 - 67
381(chain C and (resid 3:24 or resid 26:28 or resid...C69 - 73
391(chain C and (resid 3:24 or resid 26:28 or resid...C75 - 86
3101(chain C and (resid 3:24 or resid 26:28 or resid...C88 - 94
3111(chain C and (resid 3:24 or resid 26:28 or resid...C96 - 97
3121(chain C and (resid 3:24 or resid 26:28 or resid...C99 - 149
3131(chain C and (resid 3:24 or resid 26:28 or resid...C151 - 165
3141(chain C and (resid 3:24 or resid 26:28 or resid...C167 - 183
3151(chain C and (resid 3:24 or resid 26:28 or resid...C185 - 218
3161(chain C and (resid 3:24 or resid 26:28 or resid...C220 - 230
3171(chain C and (resid 3:24 or resid 26:28 or resid...C233 - 2379
3181(chain C and (resid 3:24 or resid 26:28 or resid...C281 - 290
3191(chain C and (resid 3:24 or resid 26:28 or resid...C293290
3201(chain C and (resid 3:24 or resid 26:28 or resid...C293
3211(chain C and (resid 3:24 or resid 26:28 or resid...C295 - 297
3221(chain C and (resid 3:24 or resid 26:28 or resid...C298
3231(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3241(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3251(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3261(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3271(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3281(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3291(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3301(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
3311(chain C and (resid 3:24 or resid 26:28 or resid...C3 - 298
411(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 24
421(chain D and (resid 3:24 or resid 26:28 or resid...D26 - 28
431(chain D and (resid 3:24 or resid 26:28 or resid...D30 - 31
441(chain D and (resid 3:24 or resid 26:28 or resid...D33 - 50
451(chain D and (resid 3:24 or resid 26:28 or resid...D52 - 55
461(chain D and (resid 3:24 or resid 26:28 or resid...D58 - 59
471(chain D and (resid 3:24 or resid 26:28 or resid...D61 - 67
481(chain D and (resid 3:24 or resid 26:28 or resid...D69 - 73
491(chain D and (resid 3:24 or resid 26:28 or resid...D75 - 86
4101(chain D and (resid 3:24 or resid 26:28 or resid...D88 - 94
4111(chain D and (resid 3:24 or resid 26:28 or resid...D96 - 97
4121(chain D and (resid 3:24 or resid 26:28 or resid...D99 - 149
4131(chain D and (resid 3:24 or resid 26:28 or resid...D151 - 165
4141(chain D and (resid 3:24 or resid 26:28 or resid...D167 - 183
4151(chain D and (resid 3:24 or resid 26:28 or resid...D185 - 218
4161(chain D and (resid 3:24 or resid 26:28 or resid...D220 - 230
4171(chain D and (resid 3:24 or resid 26:28 or resid...D233 - 2379
4181(chain D and (resid 3:24 or resid 26:28 or resid...D281 - 290
4191(chain D and (resid 3:24 or resid 26:28 or resid...D293290
4201(chain D and (resid 3:24 or resid 26:28 or resid...D293
4211(chain D and (resid 3:24 or resid 26:28 or resid...D295 - 297
4221(chain D and (resid 3:24 or resid 26:28 or resid...D298
4231(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4241(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4251(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4261(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4271(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4281(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4291(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4301(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
4311(chain D and (resid 3:24 or resid 26:28 or resid...D3 - 298
511(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 24
521(chain E and (resid 3:24 or resid 26:28 or resid...E26 - 28
531(chain E and (resid 3:24 or resid 26:28 or resid...E30 - 31
541(chain E and (resid 3:24 or resid 26:28 or resid...E33 - 50
551(chain E and (resid 3:24 or resid 26:28 or resid...E52 - 55
561(chain E and (resid 3:24 or resid 26:28 or resid...E58 - 59
571(chain E and (resid 3:24 or resid 26:28 or resid...E61 - 67
581(chain E and (resid 3:24 or resid 26:28 or resid...E69 - 73
591(chain E and (resid 3:24 or resid 26:28 or resid...E75 - 86
5101(chain E and (resid 3:24 or resid 26:28 or resid...E88 - 94
5111(chain E and (resid 3:24 or resid 26:28 or resid...E96 - 97
5121(chain E and (resid 3:24 or resid 26:28 or resid...E99 - 149
5131(chain E and (resid 3:24 or resid 26:28 or resid...E151 - 165
5141(chain E and (resid 3:24 or resid 26:28 or resid...E167 - 183
5151(chain E and (resid 3:24 or resid 26:28 or resid...E185 - 218
5161(chain E and (resid 3:24 or resid 26:28 or resid...E220 - 230
5171(chain E and (resid 3:24 or resid 26:28 or resid...E233 - 2379
5181(chain E and (resid 3:24 or resid 26:28 or resid...E281 - 290
5191(chain E and (resid 3:24 or resid 26:28 or resid...E293290
5201(chain E and (resid 3:24 or resid 26:28 or resid...E293
5211(chain E and (resid 3:24 or resid 26:28 or resid...E295 - 297
5221(chain E and (resid 3:24 or resid 26:28 or resid...E298
5231(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5241(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5251(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5261(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5271(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5281(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5291(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5301(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
5311(chain E and (resid 3:24 or resid 26:28 or resid...E3 - 298
611(chain F and (resid 3:24 or resid 26:28 or resid...F3 - 24
621(chain F and (resid 3:24 or resid 26:28 or resid...F26 - 28
631(chain F and (resid 3:24 or resid 26:28 or resid...F30 - 31
641(chain F and (resid 3:24 or resid 26:28 or resid...F33 - 50
651(chain F and (resid 3:24 or resid 26:28 or resid...F58 - 59
661(chain F and (resid 3:24 or resid 26:28 or resid...F61 - 67
671(chain F and (resid 3:24 or resid 26:28 or resid...F69 - 73
681(chain F and (resid 3:24 or resid 26:28 or resid...F75 - 86
691(chain F and (resid 3:24 or resid 26:28 or resid...F88 - 94
6101(chain F and (resid 3:24 or resid 26:28 or resid...F96 - 97
6111(chain F and (resid 3:24 or resid 26:28 or resid...F2 - 298
6121(chain F and (resid 3:24 or resid 26:28 or resid...F2 - 298
6131(chain F and (resid 3:24 or resid 26:28 or resid...F185 - 218
6141(chain F and (resid 3:24 or resid 26:28 or resid...F220 - 230
6151(chain F and (resid 3:24 or resid 26:28 or resid...F233 - 2349
6161(chain F and (resid 3:24 or resid 26:28 or resid...F281 - 29
6171(chain F and (resid 3:24 or resid 26:28 or resid...F281 - 290
6181(chain F and (resid 3:24 or resid 26:28 or resid...F293
6191(chain F and (resid 3:24 or resid 26:28 or resid...F295 - 298

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

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


Mass: 34233.320 Da / Num. of mol.: 6 / Mutation: H56W
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

-
Non-polymers , 8 types, 1009 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.3 / Details: 0.2 M Magnesium acetate, 14 % PEG8000 (pH 7.3)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 28, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→46.298 Å / Num. obs: 142098 / % possible obs: 98.1 % / Redundancy: 15 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.71
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.8396 / Num. unique obs: 14097 / % possible all: 98.1

-
Processing

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

4ly8


Resolution: 1.95→46.298 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 7105 5 %
Rwork0.174 134973 -
obs0.1757 142078 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.63 Å2 / Biso mean: 30.4698 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 1.95→46.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13719 0 310 941 14970
Biso mean--43.74 35.37 -
Num. residues----1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614245
X-RAY DIFFRACTIONf_angle_d0.85119137
X-RAY DIFFRACTIONf_chiral_restr0.0552183
X-RAY DIFFRACTIONf_plane_restr0.0062426
X-RAY DIFFRACTIONf_dihedral_angle_d15.2788647
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7411X-RAY DIFFRACTION4.464TORSIONAL
12B7411X-RAY DIFFRACTION4.464TORSIONAL
13C7411X-RAY DIFFRACTION4.464TORSIONAL
14D7411X-RAY DIFFRACTION4.464TORSIONAL
15E7411X-RAY DIFFRACTION4.464TORSIONAL
16F7411X-RAY DIFFRACTION4.464TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.97220.37172300.3437436596
1.9722-1.99540.34852360.2928449799
1.9954-2.01970.27692390.2568452699
2.0197-2.04530.30132350.2341446599
2.0453-2.07220.27382370.2199451599
2.0722-2.10060.26012370.2113449799
2.1006-2.13060.25782390.2079453899
2.1306-2.16240.2452360.2016449299
2.1624-2.19620.23462360.2006446998
2.1962-2.23220.27692210.2062420392
2.2322-2.27070.25451790.2052341175
2.2707-2.31190.22442390.1863453599
2.3119-2.35640.21252400.17514562100
2.3564-2.40450.21922390.16414537100
2.4045-2.45680.2182400.16754570100
2.4568-2.51390.23232410.1684574100
2.5139-2.57680.21932410.16464567100
2.5768-2.64650.21412390.16654540100
2.6465-2.72430.20652390.1648454199
2.7243-2.81220.21492180.165416191
2.8122-2.91270.21072410.16894562100
2.9127-3.02930.19622420.17324596100
3.0293-3.16720.20662410.16924593100
3.1672-3.33410.21272420.17044593100
3.3341-3.54290.20442440.17054627100
3.5429-3.81640.21222420.16294600100
3.8164-4.20020.18662440.1524639100
4.2002-4.80740.17032450.14634657100
4.8074-6.05470.16762470.16654694100
6.0547-8.720.17152560.16624847100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more