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- PDB-7kh4: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kh4
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W 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: 1.75 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. / Bhagwat, A. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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)212,55295
Polymers205,4006
Non-polymers7,15289
Water20,1051116
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,89235
Polymers68,4672
Non-polymers2,42533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-5 kcal/mol
Surface area22260 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,76329
Polymers68,4672
Non-polymers2,29627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-7 kcal/mol
Surface area23260 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,89831
Polymers68,4672
Non-polymers2,43129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-32 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.410, 225.290, 199.410
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-304-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3:24 or resid 26:56 or resid...
21(chain B and (resid 3:24 or resid 26:56 or resid...
31(chain C and (resid 3:24 or resid 26:56 or resid...
41(chain D and (resid 3:24 or resid 26:56 or resid...
51(chain E and (resid 3:24 or resid 26:56 or resid...
61(chain F and (resid 3:24 or resid 26:56 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3:24 or resid 26:56 or resid...A3 - 24
121(chain A and (resid 3:24 or resid 26:56 or resid...A26 - 56
131(chain A and (resid 3:24 or resid 26:56 or resid...A58 - 59
141(chain A and (resid 3:24 or resid 26:56 or resid...A61 - 63
151(chain A and (resid 3:24 or resid 26:56 or resid...A3 - 67
161(chain A and (resid 3:24 or resid 26:56 or resid...A69 - 73
171(chain A and (resid 3:24 or resid 26:56 or resid...A75 - 94
181(chain A and (resid 3:24 or resid 26:56 or resid...A3 - 298
191(chain A and (resid 3:24 or resid 26:56 or resid...A3 - 298
1101(chain A and (resid 3:24 or resid 26:56 or resid...A220 - 230
1111(chain A and (resid 3:24 or resid 26:56 or resid...A240 - 278
1121(chain A and (resid 3:24 or resid 26:56 or resid...A240 - 279
1131(chain A and (resid 3:24 or resid 26:56 or resid...A282 - 286
1141(chain A and (resid 3:24 or resid 26:56 or resid...A289 - 291
1151(chain A and (resid 3:24 or resid 26:56 or resid...A293
1161(chain A and (resid 3:24 or resid 26:56 or resid...A295 - 298
211(chain B and (resid 3:24 or resid 26:56 or resid...B3 - 24
221(chain B and (resid 3:24 or resid 26:56 or resid...B26 - 56
231(chain B and (resid 3:24 or resid 26:56 or resid...B58 - 59
241(chain B and (resid 3:24 or resid 26:56 or resid...B61 - 63
251(chain B and (resid 3:24 or resid 26:56 or resid...B69 - 73
261(chain B and (resid 3:24 or resid 26:56 or resid...B75 - 94
271(chain B and (resid 3:24 or resid 26:56 or resid...B-5 - 298
281(chain B and (resid 3:24 or resid 26:56 or resid...B-5 - 298
291(chain B and (resid 3:24 or resid 26:56 or resid...B220 - 230
2101(chain B and (resid 3:24 or resid 26:56 or resid...B233 - 234
2111(chain B and (resid 3:24 or resid 26:56 or resid...B236 - 2389
2121(chain B and (resid 3:24 or resid 26:56 or resid...B282 - 29
2131(chain B and (resid 3:24 or resid 26:56 or resid...B282 - 286
2141(chain B and (resid 3:24 or resid 26:56 or resid...B289 - 291
2151(chain B and (resid 3:24 or resid 26:56 or resid...B293
2161(chain B and (resid 3:24 or resid 26:56 or resid...B295 - 298
311(chain C and (resid 3:24 or resid 26:56 or resid...C3 - 24
321(chain C and (resid 3:24 or resid 26:56 or resid...C26 - 56
331(chain C and (resid 3:24 or resid 26:56 or resid...C58 - 59
341(chain C and (resid 3:24 or resid 26:56 or resid...C61 - 63
351(chain C and (resid 3:24 or resid 26:56 or resid...C69 - 73
361(chain C and (resid 3:24 or resid 26:56 or resid...C75 - 94
371(chain C and (resid 3:24 or resid 26:56 or resid...C3 - 298
381(chain C and (resid 3:24 or resid 26:56 or resid...C3 - 298
391(chain C and (resid 3:24 or resid 26:56 or resid...C220 - 230
3101(chain C and (resid 3:24 or resid 26:56 or resid...C233 - 234
3111(chain C and (resid 3:24 or resid 26:56 or resid...C236 - 2389
3121(chain C and (resid 3:24 or resid 26:56 or resid...C282 - 29
3131(chain C and (resid 3:24 or resid 26:56 or resid...C282 - 286
3141(chain C and (resid 3:24 or resid 26:56 or resid...C289 - 291
3151(chain C and (resid 3:24 or resid 26:56 or resid...C293
3161(chain C and (resid 3:24 or resid 26:56 or resid...C295 - 298
411(chain D and (resid 3:24 or resid 26:56 or resid...D3 - 24
421(chain D and (resid 3:24 or resid 26:56 or resid...D26 - 56
431(chain D and (resid 3:24 or resid 26:56 or resid...D58 - 59
441(chain D and (resid 3:24 or resid 26:56 or resid...D61 - 63
451(chain D and (resid 3:24 or resid 26:56 or resid...D69 - 73
461(chain D and (resid 3:24 or resid 26:56 or resid...D75 - 94
471(chain D and (resid 3:24 or resid 26:56 or resid...D-5 - 298
481(chain D and (resid 3:24 or resid 26:56 or resid...D-5 - 298
491(chain D and (resid 3:24 or resid 26:56 or resid...D220 - 230
4101(chain D and (resid 3:24 or resid 26:56 or resid...D233 - 234
4111(chain D and (resid 3:24 or resid 26:56 or resid...D236 - 2389
4121(chain D and (resid 3:24 or resid 26:56 or resid...D282 - 29
4131(chain D and (resid 3:24 or resid 26:56 or resid...D282 - 286
4141(chain D and (resid 3:24 or resid 26:56 or resid...D289 - 291
4151(chain D and (resid 3:24 or resid 26:56 or resid...D293
4161(chain D and (resid 3:24 or resid 26:56 or resid...D295 - 298
511(chain E and (resid 3:24 or resid 26:56 or resid...E3 - 24
521(chain E and (resid 3:24 or resid 26:56 or resid...E26 - 56
531(chain E and (resid 3:24 or resid 26:56 or resid...E58 - 59
541(chain E and (resid 3:24 or resid 26:56 or resid...E61 - 63
551(chain E and (resid 3:24 or resid 26:56 or resid...E69 - 73
561(chain E and (resid 3:24 or resid 26:56 or resid...E75 - 94
571(chain E and (resid 3:24 or resid 26:56 or resid...E2 - 298
581(chain E and (resid 3:24 or resid 26:56 or resid...E2 - 298
591(chain E and (resid 3:24 or resid 26:56 or resid...E220 - 230
5101(chain E and (resid 3:24 or resid 26:56 or resid...E233 - 234
5111(chain E and (resid 3:24 or resid 26:56 or resid...E236 - 2389
5121(chain E and (resid 3:24 or resid 26:56 or resid...E282 - 29
5131(chain E and (resid 3:24 or resid 26:56 or resid...E282 - 286
5141(chain E and (resid 3:24 or resid 26:56 or resid...E289 - 291
5151(chain E and (resid 3:24 or resid 26:56 or resid...E293
5161(chain E and (resid 3:24 or resid 26:56 or resid...E295 - 298
611(chain F and (resid 3:24 or resid 26:56 or resid...F3 - 24
621(chain F and (resid 3:24 or resid 26:56 or resid...F26 - 56
631(chain F and (resid 3:24 or resid 26:56 or resid...F58 - 59
641(chain F and (resid 3:24 or resid 26:56 or resid...F61 - 63
651(chain F and (resid 3:24 or resid 26:56 or resid...F69 - 73
661(chain F and (resid 3:24 or resid 26:56 or resid...F75 - 94
671(chain F and (resid 3:24 or resid 26:56 or resid...F3 - 298
681(chain F and (resid 3:24 or resid 26:56 or resid...F3 - 298
691(chain F and (resid 3:24 or resid 26:56 or resid...F220 - 230
6101(chain F and (resid 3:24 or resid 26:56 or resid...F233 - 234
6111(chain F and (resid 3:24 or resid 26:56 or resid...F236 - 2389
6121(chain F and (resid 3:24 or resid 26:56 or resid...F282 - 29
6131(chain F and (resid 3:24 or resid 26:56 or resid...F282 - 286
6141(chain F and (resid 3:24 or resid 26:56 or resid...F289 - 291
6151(chain F and (resid 3:24 or resid 26:56 or resid...F293
6161(chain F and (resid 3:24 or resid 26:56 or resid...F295 - 298

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Components

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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

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Non-polymers , 9 types, 1205 molecules

#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 288.15 K / Method: microbatch
Details: 0.2 M Magnesium acetate, 14 % PEG8000 (pH 7.3), 120 mMR, R-BisLysine
PH range: 7.3

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2018
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: 1.75→48.896 Å / Num. obs: 190178 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 21.38 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.84
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 0.6044 / Num. unique obs: 18744 / % possible all: 99.41

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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: 1.75→48.896 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 9507 5 %
Rwork0.1566 180643 -
obs0.158 190150 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.44 Å2 / Biso mean: 22.087 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.75→48.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13844 0 463 1116 15423
Biso mean--35.76 29.25 -
Num. residues----1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914480
X-RAY DIFFRACTIONf_angle_d1.12519406
X-RAY DIFFRACTIONf_chiral_restr0.0652202
X-RAY DIFFRACTIONf_plane_restr0.0092454
X-RAY DIFFRACTIONf_dihedral_angle_d15.5688760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7593X-RAY DIFFRACTION7.465TORSIONAL
12B7593X-RAY DIFFRACTION7.465TORSIONAL
13C7593X-RAY DIFFRACTION7.465TORSIONAL
14D7593X-RAY DIFFRACTION7.465TORSIONAL
15E7593X-RAY DIFFRACTION7.465TORSIONAL
16F7593X-RAY DIFFRACTION7.465TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.76990.34973120.3034593099
1.7699-1.79070.29383130.2724594799
1.7907-1.81260.29133120.24755920100
1.8126-1.83550.2533170.22136015100
1.8355-1.85970.23023120.19915945100
1.8597-1.88520.23733160.19355990100
1.8852-1.91210.21163150.17765988100
1.9121-1.94060.19693150.16265976100
1.9406-1.9710.2063160.16456008100
1.971-2.00330.19993150.15885979100
2.0033-2.03780.19743140.15475980100
2.0378-2.07490.19333170.15286010100
2.0749-2.11480.20773150.15025997100
2.1148-2.15790.17993140.14825968100
2.1579-2.20490.18863160.14745986100
2.2049-2.25620.18273160.14376022100
2.2562-2.31260.17673170.15016011100
2.3126-2.37510.19343150.14885995100
2.3751-2.4450.17383170.14816016100
2.445-2.52390.193160.14686001100
2.5239-2.61410.19453190.14026060100
2.6141-2.71880.1563160.13896006100
2.7188-2.84250.18773180.14796039100
2.8425-2.99230.1753180.15236039100
2.9923-3.17980.18513180.1526047100
3.1798-3.42520.17543190.15556067100
3.4252-3.76980.15583210.14896088100
3.7698-4.3150.15413210.14236101100
4.315-5.43530.18243240.15216164100
5.4353-7.830.17593330.16436348100

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