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- PDB-7kwp: Dihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate ... -

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Basic information

Entry
Database: PDB / ID: 7kwp
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE
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
LYSINE / 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: 2.26 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

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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)206,70725
Polymers205,1126
Non-polymers1,59619
Water8,053447
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)137,98020
Polymers136,7414
Non-polymers1,23916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-85 kcal/mol
Surface area38580 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)137,45410
Polymers136,7414
Non-polymers7136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10310 Å2
ΔGint-53 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.400, 231.130, 199.730
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 290 or (resid 291...
21(chain B and (resid 3 through 290 or (resid 291...
31(chain C and (resid 3 through 290 or (resid 291...
41(chain D and (resid 3 through 165 or (resid 166...
51(chain E and (resid 3 through 165 or (resid 166...
61(chain F and (resid 3 through 290 or (resid 291...

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
11LYSLYSMETMET(chain A and (resid 3 through 290 or (resid 291...AA3 - 29015 - 302
12LYSLYSLYSLYS(chain A and (resid 3 through 290 or (resid 291...AA291303
13LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
17LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
18LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
19LYSLYSPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
21LYSLYSMETMET(chain B and (resid 3 through 290 or (resid 291...BB3 - 29015 - 302
22LYSLYSLYSLYS(chain B and (resid 3 through 290 or (resid 291...BB291303
23LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
28LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
29LYSLYSPHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
31LYSLYSMETMET(chain C and (resid 3 through 290 or (resid 291...CC3 - 29015 - 302
32LYSLYSLYSLYS(chain C and (resid 3 through 290 or (resid 291...CC291303
33LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
37LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
38LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
39LYSLYSPHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
41LYSLYSVALVAL(chain D and (resid 3 through 165 or (resid 166...DD3 - 16515 - 177
42KPIKPIKPIKPI(chain D and (resid 3 through 165 or (resid 166...DD166178
43LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
47LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
48LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
49LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
410LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
411LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
412LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
413LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
414LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
415LYSLYSPHEPHE(chain D and (resid 3 through 165 or (resid 166...DD3 - 29815 - 310
51LYSLYSVALVAL(chain E and (resid 3 through 165 or (resid 166...EE3 - 16515 - 177
52KPIKPIKPIKPI(chain E and (resid 3 through 165 or (resid 166...EE166178
53LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
57LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
58LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
59LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
510LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
511LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
512LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
513LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
514LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
515LYSLYSPHEPHE(chain E and (resid 3 through 165 or (resid 166...EE3 - 29815 - 310
61LYSLYSMETMET(chain F and (resid 3 through 290 or (resid 291...FF3 - 29015 - 302
62LYSLYSLYSLYS(chain F and (resid 3 through 290 or (resid 291...FF291303
63LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
67LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
68LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
69LYSLYSPHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 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 , 6 types, 466 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.3 M Magnesium acetate, 10 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 60 mM L-lysine

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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 30, 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: 2.26→45.84 Å / Num. obs: 92460 / % possible obs: 99.82 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 2.26→2.341 Å / Rmerge(I) obs: 0.374 / Num. unique obs: 9106 / % possible all: 99.9

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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: 2.26→45.84 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 4619 5 %
Rwork0.2443 87801 -
obs0.2459 92420 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.52 Å2 / Biso mean: 38.1087 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: final / Resolution: 2.26→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13644 0 43 447 14134
Biso mean--21.4 38.77 -
Num. residues----1782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION4.488TORSIONAL
12B5358X-RAY DIFFRACTION4.488TORSIONAL
13C5358X-RAY DIFFRACTION4.488TORSIONAL
14D5358X-RAY DIFFRACTION4.488TORSIONAL
15E5358X-RAY DIFFRACTION4.488TORSIONAL
16F5358X-RAY DIFFRACTION4.488TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.290.32211520.293428883040100
2.29-2.310.33571530.302129083061100
2.31-2.340.30551500.279828553005100
2.34-2.370.35321550.280129423097100
2.37-2.40.32731510.273228823033100
2.4-2.430.32451530.262129053058100
2.43-2.470.32251520.275529003052100
2.47-2.510.33191530.265729023055100
2.51-2.550.32171520.271328803032100
2.55-2.590.33661540.264129363090100
2.59-2.630.31911520.26328883040100
2.63-2.680.311540.265229263080100
2.68-2.730.3351530.264729083061100
2.73-2.790.30081530.277229033056100
2.79-2.850.31371530.273729053058100
2.85-2.910.30421530.288129043057100
2.91-2.990.3091540.28829203074100
2.99-3.070.3641540.281629363090100
3.07-3.160.27951530.280629153068100
3.16-3.260.3331540.274229173071100
3.26-3.380.30341540.279729193073100
3.38-3.510.2921530.281129343087100
3.51-3.670.28951550.260829383093100
3.67-3.860.26581550.233829413096100
3.86-4.110.24941560.212829603116100
4.11-4.420.2481540.210129423096100
4.42-4.870.22231550.209429423097100
4.87-5.570.26281570.220929833140100
5.57-7.010.23191580.215229993157100
7.01-45.840.16131640.16223123328799
Refinement TLS params.Method: refined / Origin x: -40.4276 Å / Origin y: -105.633 Å / Origin z: 29.4733 Å
111213212223313233
T0.3434 Å2-0.0125 Å20.0029 Å2-0.2439 Å20.0341 Å2--0.2953 Å2
L0.144 °2-0.127 °20.1151 °2-0.2747 °2-0.1816 °2--0.1557 °2
S-0.0072 Å °-0.0214 Å °-0.0084 Å °0.0179 Å °0.0209 Å °0.021 Å °0.0219 Å °-0.0226 Å °-0.0131 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 DIFFRACTION1allD3 - 298
5X-RAY DIFFRACTION1allE3 - 298
6X-RAY DIFFRACTION1allF3 - 298
7X-RAY DIFFRACTION1allG1 - 7
8X-RAY DIFFRACTION1allS1 - 502
9X-RAY DIFFRACTION1allH1 - 5
10X-RAY DIFFRACTION1allI1 - 6
11X-RAY DIFFRACTION1allJ1
12X-RAY DIFFRACTION1allK1

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