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- PDB-7kn9: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kn9
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dihydrodipicolinate synthase
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
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 / 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: 2.07 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: THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND.
Authors: Saran, S. / Majdi Yazdi, M. / Chung, I. / Sanders, D.A.R.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 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)210,15887
Polymers204,7636
Non-polymers5,39581
Water18,6281034
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,16832
Polymers68,2542
Non-polymers1,91330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-83 kcal/mol
Surface area21090 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,00429
Polymers68,2542
Non-polymers1,74927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-24 kcal/mol
Surface area21420 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,98726
Polymers68,2542
Non-polymers1,73324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-30 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.310, 231.390, 199.640
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 18 or resid 20...
21(chain B and (resid 3 through 17 or (resid 18...
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
11LYSLYSLYSLYS(chain A and (resid 3 through 18 or resid 20...AA3 - 1815 - 30
12GLYGLYTHRTHR(chain A and (resid 3 through 18 or resid 20...AA20 - 7332 - 85
13LYSLYSLYSLYS(chain A and (resid 3 through 18 or resid 20...AA7486
14LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 18 or resid 20...AA3 - 29815 - 310
21LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 1715 - 29
22LYSLYSLYSLYS(chain B and (resid 3 through 17 or (resid 18...BB1830
23ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 310
24ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 310
25ASPASPPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB2 - 29814 - 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
43LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 17 or (resid 18...DD3 - 29815 - 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: 34127.223 Da / Num. of mol.: 6 / Mutation: E88A
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, 1115 molecules

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


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 M Magnesium acetate, 8 % 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 6M / Detector: PIXEL / Date: Jul 26, 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: 2.07→45.83 Å / Num. obs: 119299 / % possible obs: 99.3 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 12.44
Reflection shellResolution: 2.07→2.144 Å / Rmerge(I) obs: 0.5427 / Num. unique obs: 11198 / % possible all: 94.16

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Processing

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

4ly8


Resolution: 2.07→45.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 5965 5 %
Rwork0.1766 113317 -
obs0.1782 119282 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.47 Å2 / Biso mean: 26.9556 Å2 / Biso min: 15.21 Å2
Refinement stepCycle: final / Resolution: 2.07→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13594 0 281 1034 14909
Biso mean--36.9 30.47 -
Num. residues----1784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5250X-RAY DIFFRACTION2.39TORSIONAL
12B5250X-RAY DIFFRACTION2.39TORSIONAL
13C5250X-RAY DIFFRACTION2.39TORSIONAL
14D5250X-RAY DIFFRACTION2.39TORSIONAL
15E5250X-RAY DIFFRACTION2.39TORSIONAL
16F5250X-RAY DIFFRACTION2.39TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.07-2.090.32281810.2909343891
2.09-2.120.3041860.2691353794
2.12-2.140.30091930.2491366497
2.14-2.170.25391950.2288370499
2.17-2.20.2581970.21033759100
2.2-2.230.22011980.21113746100
2.23-2.260.22961980.20783759100
2.26-2.30.23711980.19923769100
2.3-2.330.25532000.19263796100
2.33-2.370.21531990.19253795100
2.37-2.410.2481980.1933755100
2.41-2.450.24311970.1853746100
2.45-2.50.21492020.19183822100
2.5-2.550.23891960.18133735100
2.55-2.610.22482000.18113789100
2.61-2.670.20122010.17663822100
2.67-2.740.24011980.18333777100
2.74-2.810.22531990.17843766100
2.81-2.890.20681990.18513787100
2.89-2.990.2452000.18213792100
2.99-3.090.20572010.1743826100
3.09-3.220.20591990.17753789100
3.22-3.360.20222000.18443799100
3.36-3.540.21842020.17893833100
3.54-3.760.16542010.16193827100
3.76-4.050.18632020.15143833100
4.05-4.460.16712020.14523838100
4.46-5.10.17282040.14483873100
5.1-6.430.1882060.17333904100
6.43-100.16392130.14824037100

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