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- PDB-7km0: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A mutant w... -

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Basic information

Entry
Database: PDB / ID: 7km0
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H59A mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric 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
Chem-3VN / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME
Authors: Saran, S. / Skovpen, Y. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionNov 2, 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)206,52720
Polymers204,7096
Non-polymers1,81714
Water7,584421
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,09911
Polymers68,2362
Non-polymers8629
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-5 kcal/mol
Surface area21520 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8736
Polymers68,2362
Non-polymers6374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-16 kcal/mol
Surface area21320 Å2
MethodPISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5553
Polymers68,2362
Non-polymers3181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-22 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.896, 230.396, 201.723
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
11E-474-

HOH

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 17 or (resid 18...
31(chain C and (resid 3 through 57 or (resid 58...
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
14LYSLYSPHEPHE(chain A and (resid 3 through 17 or (resid 18...AA3 - 29815 - 310
15LYSLYSPHEPHE(chain A and (resid 3 through 17 or (resid 18...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
23LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
24LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
25LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
26LYSLYSPHEPHE(chain B and (resid 3 through 17 or (resid 18...BB3 - 29815 - 310
31LYSLYSGLUGLU(chain C and (resid 3 through 57 or (resid 58...CC3 - 5715 - 69
32GLUGLUGLUGLU(chain C and (resid 3 through 57 or (resid 58...CC5870
33ALAALAALAALA(chain C and (resid 3 through 57 or (resid 58...CC5971
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
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
63LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
64LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
65LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...FF3 - 29815 - 310
66LYSLYSPHEPHE(chain F and (resid 3 through 17 or (resid 18...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: 34118.191 Da / Num. of mol.: 6 / Mutation: H59A
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, 435 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30N4O4
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 48.95 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.9 M Magnesium acetate, 8 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 120 mM R,R-bisLysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→21.3 Å / Num. obs: 61037 / % possible obs: 94.03 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 2.027 / Num. unique obs: 6010

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Processing

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

4ly8


Resolution: 2.6→21.3 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 3046 5.05 %
Rwork0.2348 57232 -
obs0.2377 60278 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.81 Å2 / Biso mean: 16.7737 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 2.6→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13565 0 122 421 14108
Biso mean--16.45 15.05 -
Num. residues----1776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5316X-RAY DIFFRACTION4.709TORSIONAL
12B5316X-RAY DIFFRACTION4.709TORSIONAL
13C5316X-RAY DIFFRACTION4.709TORSIONAL
14D5316X-RAY DIFFRACTION4.709TORSIONAL
15E5316X-RAY DIFFRACTION4.709TORSIONAL
16F5316X-RAY DIFFRACTION4.709TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.640.38311250.3059242793
2.64-2.680.3821230.3011247595
2.68-2.730.38161360.288249195
2.73-2.780.35991420.2854250996
2.78-2.830.39641320.28254998
2.83-2.890.30511460.2737253899
2.89-2.950.35971430.263258499
2.95-3.020.32091320.25672621100
3.02-3.10.34561440.25422596100
3.1-3.180.33451370.24752636100
3.18-3.270.33921490.24662609100
3.27-3.380.29951360.24412623100
3.38-3.50.30841430.248261099
3.5-3.640.30261320.23712595100
3.64-3.80.28621260.2283263699
3.8-40.27141290.22052645100
4-4.250.24011550.20772630100
4.25-4.580.22091280.19222642100
4.58-5.030.24251430.1952666100
5.03-5.750.27581550.20662657100
5.75-7.190.23951520.20672693100
7.2-100.16471380.16442800100

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