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- PDB-5f1u: biomimetic design results in a potent allosteric inhibitor of dih... -

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Basic information

Entry
Database: PDB / ID: 5f1u
Titlebiomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from Campylobacter jejuni
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE/LYASE inhibitor / schiff-base / aldolase / TIM barrel / LYASE-LYASE inhibitor complex
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3VN / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsConly, C.J.T. / Palmer, D.R.J. / Sanders, D.A.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni.
Authors: Skovpen, Y.V. / Conly, C.J. / Sanders, D.A. / Palmer, D.R.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,89119
Polymers130,2544
Non-polymers1,63715
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-42 kcal/mol
Surface area39450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.590, 96.780, 145.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 32563.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dapA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 6 types, 317 molecules

#2: Chemical ChemComp-3VN / (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid / bis-Lysine


Mass: 318.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30N4O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAuthors state that in ligand 3VN, carbonyl groups are de-protonated, and amine groups are protonated.

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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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.28 M NaAct, 0.1 mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 1, 2013
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 47688 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.22 % / Biso Wilson estimate: 30.33 Å2 / Rmerge F obs: 0.991 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.324 / Χ2: 1.017 / Net I/σ(I): 11.71 / Num. measured all: 839254
Reflection shellResolution: 2.35→2.41 Å / Rmerge F obs: 0.005 / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 3.56 / Num. measured obs: 10632 / Num. possible: 26965 / Num. unique obs: 5464 / Rrim(I) all: 18.744 / Rejects: 0 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9_1692refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LER

3ler


Resolution: 2.35→48.39 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 2384 5 %
Rwork0.1706 45295 -
obs0.1735 47679 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.6 Å2 / Biso mean: 34.4077 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 2.35→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9091 0 108 302 9501
Biso mean--45.81 35.33 -
Num. residues----1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039348
X-RAY DIFFRACTIONf_angle_d0.83412609
X-RAY DIFFRACTIONf_chiral_restr0.0321458
X-RAY DIFFRACTIONf_plane_restr0.0041607
X-RAY DIFFRACTIONf_dihedral_angle_d14.4563517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.39790.29611380.214926112749
2.3979-2.45010.27641380.213326182756
2.4501-2.50710.25521370.192826312768
2.5071-2.56980.24731390.199626382777
2.5698-2.63920.28061380.178726292767
2.6392-2.71690.2661390.187526412780
2.7169-2.80460.25721380.178826162754
2.8046-2.90480.25031390.186826462785
2.9048-3.02110.23951390.178726422781
3.0211-3.15860.22921400.175526542794
3.1586-3.32510.2831410.1826842825
3.3251-3.53330.24421390.181226402779
3.5333-3.8060.23351410.165926762817
3.806-4.18890.20031420.154126852827
4.1889-4.79450.18361410.143926862827
4.7945-6.03880.21941440.16327442888
6.0388-48.40020.18341510.153528543005
Refinement TLS params.Method: refined / Origin x: -6.451 Å / Origin y: 3.4065 Å / Origin z: 54.4349 Å
111213212223313233
T0.149 Å20.012 Å20.016 Å2-0.1338 Å20.0089 Å2--0.1388 Å2
L0.1405 °20.0538 °2-0.0281 °2-0.2904 °2-0.0217 °2--0.2606 °2
S-0.0017 Å °0.0064 Å °0.0261 Å °0.0915 Å °-0.0023 Å °0.0182 Å °-0.001 Å °-0.0052 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 298
2X-RAY DIFFRACTION1allB4 - 298
3X-RAY DIFFRACTION1allC3 - 298
4X-RAY DIFFRACTION1allD3 - 298
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allM1
13X-RAY DIFFRACTION1allO1
14X-RAY DIFFRACTION1allS1 - 347
15X-RAY DIFFRACTION1allN1
16X-RAY DIFFRACTION1allP1
17X-RAY DIFFRACTION1allQ1
18X-RAY DIFFRACTION1allT1
19X-RAY DIFFRACTION1allU1
20X-RAY DIFFRACTION1allV1

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