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

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Basic information

Entry
Database: PDB / ID: 7lcf
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, with pyruvate bound in the active site and L-lysine bound at the allosteric site in C121 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 / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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-factors: L- lysine and R, R- bisLysine allosterically inhibit Cj. DHDPS Enzyme by decreasing its protein dynamics
Authors: Saran, S. / Sanders, D.A.R.
History
DepositionJan 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: 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
G: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,01425
Polymers410,22312
Non-polymers1,79113
Water9,998555
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
G: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3308
Polymers136,7414
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-60 kcal/mol
Surface area39670 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
K: 4-hydroxy-tetrahydrodipicolinate synthase
L: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3308
Polymers136,7414
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-63 kcal/mol
Surface area39470 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
H: 4-hydroxy-tetrahydrodipicolinate synthase
I: 4-hydroxy-tetrahydrodipicolinate synthase
J: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3549
Polymers136,7414
Non-polymers6135
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-71 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.020, 85.890, 200.220
Angle α, β, γ (deg.)90.000, 89.920, 90.000
Int Tables number5
Space group name H-MC121
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 290 or (resid 291...
51(chain E and (resid 3 through 290 or (resid 291...
61(chain F and (resid 3 through 290 or (resid 291...
71(chain G and (resid 3 through 290 or (resid 291...
81(chain H and (resid 3 through 290 or (resid 291...
91chain I
101(chain J and (resid 3 through 290 or (resid 291...
111(chain K and (resid 3 through 290 or (resid 291...
121(chain L 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
13ASPASPPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA2 - 29814 - 310
14ASPASPPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA2 - 29814 - 310
15ASPASPPHEPHE(chain A and (resid 3 through 290 or (resid 291...AA2 - 29814 - 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
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
41LYSLYSMETMET(chain D and (resid 3 through 290 or (resid 291...DD3 - 29015 - 302
42LYSLYSLYSLYS(chain D and (resid 3 through 290 or (resid 291...DD291303
43LYSLYSPHEPHE(chain D and (resid 3 through 290 or (resid 291...DD3 - 29815 - 310
44LYSLYSPHEPHE(chain D and (resid 3 through 290 or (resid 291...DD3 - 29815 - 310
45LYSLYSPHEPHE(chain D and (resid 3 through 290 or (resid 291...DD3 - 29815 - 310
51LYSLYSMETMET(chain E and (resid 3 through 290 or (resid 291...EE3 - 29015 - 302
52LYSLYSLYSLYS(chain E and (resid 3 through 290 or (resid 291...EE291303
53LYSLYSPHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
54LYSLYSPHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
55LYSLYSPHEPHE(chain E and (resid 3 through 290 or (resid 291...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
71LYSLYSMETMET(chain G and (resid 3 through 290 or (resid 291...GG3 - 29015 - 302
72LYSLYSLYSLYS(chain G and (resid 3 through 290 or (resid 291...GG291303
73LYSLYSPHEPHE(chain G and (resid 3 through 290 or (resid 291...GG3 - 29815 - 310
74LYSLYSPHEPHE(chain G and (resid 3 through 290 or (resid 291...GG3 - 29815 - 310
75LYSLYSPHEPHE(chain G and (resid 3 through 290 or (resid 291...GG3 - 29815 - 310
81LYSLYSMETMET(chain H and (resid 3 through 290 or (resid 291...HH3 - 29015 - 302
82LYSLYSLYSLYS(chain H and (resid 3 through 290 or (resid 291...HH291303
83LYSLYSPHEPHE(chain H and (resid 3 through 290 or (resid 291...HH3 - 29815 - 310
84LYSLYSPHEPHE(chain H and (resid 3 through 290 or (resid 291...HH3 - 29815 - 310
85LYSLYSPHEPHE(chain H and (resid 3 through 290 or (resid 291...HH3 - 29815 - 310
91LYSLYSPHEPHEchain III3 - 29815 - 310
101LYSLYSMETMET(chain J and (resid 3 through 290 or (resid 291...JJ3 - 29015 - 302
102LYSLYSLYSLYS(chain J and (resid 3 through 290 or (resid 291...JJ291303
103LYSLYSPHEPHE(chain J and (resid 3 through 290 or (resid 291...JJ3 - 29815 - 310
104LYSLYSPHEPHE(chain J and (resid 3 through 290 or (resid 291...JJ3 - 29815 - 310
105LYSLYSPHEPHE(chain J and (resid 3 through 290 or (resid 291...JJ3 - 29815 - 310
111LYSLYSMETMET(chain K and (resid 3 through 290 or (resid 291...KK3 - 29015 - 302
112LYSLYSLYSLYS(chain K and (resid 3 through 290 or (resid 291...KK291303
113LYSLYSPHEPHE(chain K and (resid 3 through 290 or (resid 291...KK3 - 29815 - 310
114LYSLYSPHEPHE(chain K and (resid 3 through 290 or (resid 291...KK3 - 29815 - 310
115LYSLYSPHEPHE(chain K and (resid 3 through 290 or (resid 291...KK3 - 29815 - 310
121LYSLYSMETMET(chain L and (resid 3 through 290 or (resid 291...LL3 - 29015 - 302
122LYSLYSLYSLYS(chain L and (resid 3 through 290 or (resid 291...LL291303
123LYSLYSPHEPHE(chain L and (resid 3 through 290 or (resid 291...LL3 - 29815 - 310
124LYSLYSPHEPHE(chain L and (resid 3 through 290 or (resid 291...LL3 - 29815 - 310
125LYSLYSPHEPHE(chain L and (resid 3 through 290 or (resid 291...LL3 - 29815 - 310

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34185.258 Da / Num. of mol.: 12
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
#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.7 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: Jul 25, 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: 2.69→45.98 Å / Num. obs: 108564 / % possible obs: 98.81 % / Redundancy: 15 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.1102 / Rpim(I) all: 0.1102 / Net I/σ(I): 5.6
Reflection shellResolution: 2.69→2.786 Å / Rmerge(I) obs: 0.5034 / Num. unique obs: 10831 / CC1/2: 0.699 / CC star: 0.907 / Rpim(I) all: 0.5034 / Rrim(I) all: 0.7119 / % possible all: 99.66

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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: 2.69→45.98 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 5426 5 %
Rwork0.2273 103086 -
obs0.2294 108512 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.48 Å2 / Biso mean: 43.3547 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.69→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27296 0 21 555 27872
Biso mean--20.48 37.95 -
Num. residues----3563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10668X-RAY DIFFRACTION4.832TORSIONAL
12B10668X-RAY DIFFRACTION4.832TORSIONAL
13C10668X-RAY DIFFRACTION4.832TORSIONAL
14D10668X-RAY DIFFRACTION4.832TORSIONAL
15E10668X-RAY DIFFRACTION4.832TORSIONAL
16F10668X-RAY DIFFRACTION4.832TORSIONAL
17G10668X-RAY DIFFRACTION4.832TORSIONAL
18H10668X-RAY DIFFRACTION4.832TORSIONAL
19I10668X-RAY DIFFRACTION4.832TORSIONAL
110J10668X-RAY DIFFRACTION4.832TORSIONAL
111K10668X-RAY DIFFRACTION4.832TORSIONAL
112L10668X-RAY DIFFRACTION4.832TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.69-2.720.3231790.27843388100
2.72-2.750.34681820.29113460100
2.75-2.790.37141810.29243436100
2.79-2.820.34311800.28733432100
2.82-2.860.3231820.29473457100
2.86-2.90.34661790.28143436100
2.9-2.940.34661820.281345999
2.94-2.980.35551790.2902340999
2.98-3.030.35631810.3072344899
3.03-3.080.35351820.288344699
3.08-3.130.32291800.2725341299
3.13-3.190.32161810.2646345599
3.19-3.250.31611800.2568341599
3.25-3.320.33871820.2655344699
3.32-3.390.34491790.2618341399
3.39-3.470.27711810.2553343299
3.47-3.550.30221810.2543343199
3.55-3.650.28551790.2427341799
3.65-3.760.26761820.2176344999
3.76-3.880.24521800.2063342198
3.88-4.020.23741780.2014337498
4.02-4.180.24141800.1991342598
4.18-4.370.23671800.1896342998
4.37-4.60.22231810.1843342298
4.6-4.890.24091810.1912344298
4.89-5.260.21571810.2002343598
5.26-5.790.25761810.2085344098
5.79-6.630.22941840.2088350199
6.63-8.340.21071820.1888345798
8-100.19311860.1907349996

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