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- PDB-7kn2: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7kn2
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, E88A 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: 2.53 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

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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)207,39842
Polymers204,7636
Non-polymers2,63536
Water7,152397
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,20414
Polymers68,2542
Non-polymers95012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-22 kcal/mol
Surface area21700 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,14114
Polymers68,2542
Non-polymers88712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-11 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)69,05314
Polymers68,2542
Non-polymers79812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-19 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.130, 232.950, 202.060
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
11C-475-

HOH

21E-459-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 24 or (resid 25...
21(chain B and (resid 3 through 20 or (resid 21...
31(chain C and (resid 3 through 20 or (resid 21...
41(chain D and (resid 3 through 20 or (resid 21...
51(chain E and (resid 3 through 20 or (resid 21...
61(chain F and (resid 3 through 20 or (resid 21...

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
11LYSLYSGLUGLU(chain A and (resid 3 through 24 or (resid 25...AA3 - 2415 - 36
12GLNGLNGLNGLN(chain A and (resid 3 through 24 or (resid 25...AA2537
13LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
14LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
16LYSLYSPHEPHE(chain A and (resid 3 through 24 or (resid 25...AA3 - 29815 - 310
21LYSLYSGLYGLY(chain B and (resid 3 through 20 or (resid 21...BB3 - 2015 - 32
22LYSLYSLYSLYS(chain B and (resid 3 through 20 or (resid 21...BB2133
23LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
27LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
28LYSLYSPHEPHE(chain B and (resid 3 through 20 or (resid 21...BB3 - 29815 - 310
31LYSLYSGLYGLY(chain C and (resid 3 through 20 or (resid 21...CC3 - 2015 - 32
32LYSLYSLYSLYS(chain C and (resid 3 through 20 or (resid 21...CC2133
33LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
34LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
35LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
36LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
37LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
38LYSLYSPHEPHE(chain C and (resid 3 through 20 or (resid 21...CC3 - 29815 - 310
41LYSLYSGLYGLY(chain D and (resid 3 through 20 or (resid 21...DD3 - 2015 - 32
42LYSLYSLYSLYS(chain D and (resid 3 through 20 or (resid 21...DD2133
43LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
46LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
47LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
48LYSLYSPHEPHE(chain D and (resid 3 through 20 or (resid 21...DD3 - 29815 - 310
51LYSLYSGLYGLY(chain E and (resid 3 through 20 or (resid 21...EE3 - 2015 - 32
52LYSLYSLYSLYS(chain E and (resid 3 through 20 or (resid 21...EE2133
53LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
56LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
57LYSLYSPHEPHE(chain E and (resid 3 through 20 or (resid 21...EE3 - 29815 - 310
61LYSLYSGLYGLY(chain F and (resid 3 through 20 or (resid 21...FF3 - 2015 - 32
62LYSLYSLYSLYS(chain F and (resid 3 through 20 or (resid 21...FF2133
63LYSLYSPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 20 or (resid 21...FF3 - 29815 - 310
67LYSLYSPHEPHE(chain F and (resid 3 through 20 or (resid 21...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: 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, 433 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / 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.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.5 M Magnesium acetate, 8 % PEG8000, 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: Aug 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: 2.53→44.05 Å / Num. obs: 67295 / % possible obs: 99.87 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 6623 / % possible all: 99.94

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Processing

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

4ly8


Resolution: 2.53→44.05 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 3362 5 %
Rwork0.2156 63908 -
obs0.2176 67270 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.04 Å2 / Biso mean: 39.0163 Å2 / Biso min: 18.89 Å2
Refinement stepCycle: final / Resolution: 2.53→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13533 0 168 397 14098
Biso mean--47.13 37.01 -
Num. residues----1776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5358X-RAY DIFFRACTION2.559TORSIONAL
12B5358X-RAY DIFFRACTION2.559TORSIONAL
13C5358X-RAY DIFFRACTION2.559TORSIONAL
14D5358X-RAY DIFFRACTION2.559TORSIONAL
15E5358X-RAY DIFFRACTION2.559TORSIONAL
16F5358X-RAY DIFFRACTION2.559TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.53-2.570.32971380.26172633100
2.57-2.60.33521380.26232620100
2.6-2.650.37361390.26142644100
2.65-2.690.34471390.26592628100
2.69-2.730.30491390.26362644100
2.73-2.780.29611390.26142633100
2.78-2.840.35571400.25712660100
2.84-2.90.3151360.27522594100
2.9-2.960.33051410.272676100
2.96-3.030.28011390.27012646100
3.03-3.10.38161390.30252640100
3.1-3.190.35381390.27212632100
3.19-3.280.31391400.25622668100
3.28-3.390.27491390.24032636100
3.39-3.510.24861390.23152644100
3.51-3.650.26371410.22482675100
3.65-3.810.21981390.20962647100
3.81-4.020.23371410.19122677100
4.02-4.270.22631410.17412664100
4.27-4.60.21231410.16552687100
4.6-5.060.19721410.16762683100
5.06-5.790.22051420.18722701100
5.79-7.290.2021440.18252740100
7.29-100.14251480.1424283699

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