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- PDB-7kwn: Dihydrodipicolinate synthase from C. jejuni with pyruvate bound t... -

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Basic information

Entry
Database: PDB / ID: 7kwn
TitleDihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site in C2221 space group
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE
Function / homology
Function and homology information


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: 2.24 Å
AuthorsSaran, S. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS.
Authors: Saran, S. / Sanders, D.A.R.
History
DepositionDec 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,71636
Polymers205,1126
Non-polymers2,60430
Water12,106672
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)138,58826
Polymers136,7414
Non-polymers1,84622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-43 kcal/mol
Surface area40280 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)138,25720
Polymers136,7414
Non-polymers1,51616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12790 Å2
ΔGint-23 kcal/mol
Surface area40760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.990, 230.190, 200.140
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 through 17 or (resid 18...
21(chain B and (resid 3 through 24 or resid 26...
31(chain C and (resid 3 through 17 or (resid 18...
41(chain D and (resid 3 through 17 or (resid 18...
51(chain E and (resid 3 through 17 or (resid 18...
61(chain F and (resid 3 through 17 or (resid 18...

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
11LYSLYSPHEPHE(chain A and (resid 3 through 17 or (resid 18...AA3 - 1715 - 29
12LYSLYSLYSLYS(chain A and (resid 3 through 17 or (resid 18...AA1830
13LYSLYSPHEPHE(chain A and (resid 3 through 17 or (resid 18...AA3 - 29815 - 310
21LYSLYSGLUGLU(chain B and (resid 3 through 24 or resid 26...BB3 - 2415 - 36
22SERSERTHRTHR(chain B and (resid 3 through 24 or resid 26...BB26 - 7338 - 85
23LYSLYSLYSLYS(chain B and (resid 3 through 24 or resid 26...BB7486
24LYSLYSPHEPHE(chain B and (resid 3 through 24 or resid 26...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 24 or resid 26...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 24 or resid 26...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 24 or resid 26...BB3 - 29815 - 310
31LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 1715 - 29
32LYSLYSLYSLYS(chain C and (resid 3 through 17 or (resid 18...CC1830
33LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 17 or (resid 18...CC3 - 29815 - 310
41LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 1715 - 29
42LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD1830
43ASPASPPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD2 - 29814 - 310
44ASPASPPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD2 - 29814 - 310
45ASPASPPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD2 - 29814 - 310
46ASPASPPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD2 - 29814 - 310
51LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 1715 - 29
52LYSLYSLYSLYS(chain E and (resid 3 through 17 or (resid 18...EE1830
53LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 17 or (resid 18...EE3 - 29815 - 310
61LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 1715 - 29
62LYSLYSLYSLYS(chain F and (resid 3 through 17 or (resid 18...FF1830
63ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF2 - 29814 - 310
64ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF2 - 29814 - 310
65ASPASPPHEPHE(chain F and (resid 3 through 17 or (resid 18...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: 34185.258 Da / Num. of mol.: 6
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, 702 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / 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.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 8 % PEG 8000, 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: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationMonochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.24→45.89 Å / Num. obs: 93275 / % possible obs: 99.89 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 11.2
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.247 / Num. unique obs: 9191 / % possible all: 99.51

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.24→45.89 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 4663 5 %
Rwork0.1773 88594 -
obs0.1792 93257 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.12 Å2 / Biso mean: 36.5486 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: final / Resolution: 2.24→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13641 0 171 672 14484
Biso mean--35.78 40.76 -
Num. residues----1778
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5322X-RAY DIFFRACTION6.519TORSIONAL
12B5322X-RAY DIFFRACTION6.519TORSIONAL
13C5322X-RAY DIFFRACTION6.519TORSIONAL
14D5322X-RAY DIFFRACTION6.519TORSIONAL
15E5322X-RAY DIFFRACTION6.519TORSIONAL
16F5322X-RAY DIFFRACTION6.519TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.24-2.270.26811540.2374292399
2.27-2.290.29311520.23782887100
2.29-2.320.29561530.2112922100
2.32-2.350.23231560.21022958100
2.35-2.380.26521530.21172899100
2.38-2.410.24881540.20262941100
2.41-2.450.26511530.19072908100
2.45-2.480.2241540.18572910100
2.48-2.520.23841550.18182959100
2.52-2.560.26221530.17422897100
2.56-2.610.21131570.1692979100
2.61-2.660.24521530.17412911100
2.66-2.710.24181550.17922946100
2.71-2.760.24931540.18092919100
2.76-2.820.23431550.18142950100
2.82-2.890.24391550.18492939100
2.89-2.960.22731530.18672918100
2.96-3.040.21631560.17972968100
3.04-3.130.20511560.17472952100
3.13-3.230.24461560.18052961100
3.23-3.350.2391550.19452944100
3.35-3.480.18581540.1812937100
3.48-3.640.21841570.18292978100
3.64-3.830.18871560.17042958100
3.83-4.070.20541550.16242961100
4.07-4.380.2011580.16022993100
4.38-4.820.18091570.15042976100
4.82-5.520.21591580.17493010100
5.52-6.950.20421600.18643046100
6.95-100.1741660.1599314499
Refinement TLS params.Method: refined / Origin x: 1.9963 Å / Origin y: 9.7044 Å / Origin z: 29.5946 Å
111213212223313233
T0.2193 Å2-0.0185 Å20.0094 Å2-0.2325 Å20.0219 Å2--0.217 Å2
L0.1681 °2-0.2092 °20.1829 °2-0.3983 °2-0.2947 °2--0.2715 °2
S-0.0091 Å °-0.0192 Å °-0.0058 Å °0.0347 Å °0.0285 Å °0.0404 Å °0.006 Å °-0.0322 Å °-0.0235 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 298
2X-RAY DIFFRACTION1allB3 - 298
3X-RAY DIFFRACTION1allC3 - 298
4X-RAY DIFFRACTION1allD2 - 298
5X-RAY DIFFRACTION1allE3 - 298
6X-RAY DIFFRACTION1allF2 - 298
7X-RAY DIFFRACTION1allS1 - 733
8X-RAY DIFFRACTION1allG1 - 6
9X-RAY DIFFRACTION1allH1 - 3
10X-RAY DIFFRACTION1allI6 - 16
11X-RAY DIFFRACTION1allJ1 - 5
12X-RAY DIFFRACTION1allK1 - 2
13X-RAY DIFFRACTION1allL1 - 7

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