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- PDB-5f1v: biomimetic design results in a potent allosteric inhibitor of dih... -

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Basic information

Entry
Database: PDB / ID: 5f1v
Titlebiomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from Campylobacter jejuni
Components4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase
KeywordsLYASE/LYASE inhibitor / schiff-base / aldolase / TIM barrel / LYASE-LYASE inhibitor complex
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 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: 2.2 Å
AuthorsConly, C.J.T. / Palmer, D.R.J. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
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 2.0Sep 27, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 3.0May 30, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.2Sep 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
Revision 3.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,96921
Polymers130,5944
Non-polymers2,37517
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-61 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 96.950, 146.970
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 / Dihydrodipicolinate synthase / HTPA synthase


Mass: 32648.543 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 , 5 types, 418 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.: 4 / Source method: obtained synthetically / Formula: C14H30N4O4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 16% PEG 4000, 0.2 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: 0.9798 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: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59651 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 1.34 % / Biso Wilson estimate: 22.62 Å2 / Rmerge F obs: 0.983 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.397 / Χ2: 1.015 / Net I/σ(I): 11.79 / Num. measured all: 1110812
Reflection shellResolution: 2.2→2.26 Å / Rmerge F obs: 0.034 / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 3.44 / Num. measured obs: 13656 / Num. possible: 38523 / Num. unique obs: 7716 / Rrim(I) all: 24.807 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_1378refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LER

3ler


Resolution: 2.2→48.47 Å / FOM work R set: 0.9035 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 2982 5 %
Rwork0.1571 56664 -
obs0.1594 59646 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.13 Å2 / Biso mean: 24.6 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 2.2→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9115 0 160 401 9676
Biso mean--40.97 28.87 -
Num. residues----1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059444
X-RAY DIFFRACTIONf_angle_d0.99212742
X-RAY DIFFRACTIONf_chiral_restr0.0661465
X-RAY DIFFRACTIONf_plane_restr0.0041620
X-RAY DIFFRACTIONf_dihedral_angle_d14.1513559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.2360.19041390.169526342773
2.236-2.27460.26331390.171226562795
2.2746-2.31590.21211420.167726922834
2.3159-2.36050.22371400.167126492789
2.3605-2.40870.23021400.156826682808
2.4087-2.4610.2131410.164926732814
2.461-2.51830.20621390.154726542793
2.5183-2.58130.2241420.145926852827
2.5813-2.6510.19791390.144526522791
2.651-2.7290.21021420.152126972839
2.729-2.81710.2031410.15126792820
2.8171-2.91780.19711420.158126862828
2.9178-3.03460.20891410.164126902831
3.0346-3.17270.21711410.158426842825
3.1727-3.33990.19331430.155227042847
3.3399-3.54910.2011410.155426842825
3.5491-3.8230.20011440.152427252869
3.823-4.20760.18591440.148427492893
4.2076-4.8160.2011430.14927192862
4.816-6.06570.20971470.170427852932
6.0657-48.48670.17041520.161828993051
Refinement TLS params.Method: refined / Origin x: 6.3131 Å / Origin y: 3.3139 Å / Origin z: 18.5231 Å
111213212223313233
T0.1398 Å2-0.0164 Å2-0.0008 Å2-0.1089 Å20.002 Å2--0.129 Å2
L0.31 °2-0.1109 °2-0.0591 °2-0.3971 °20.1059 °2--0.3831 °2
S0.0008 Å °0.0141 Å °0.0364 Å °-0.0652 Å °-0.0016 Å °-0.0403 Å °-0.0242 Å °0.0242 Å °0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 298
2X-RAY DIFFRACTION1allB2 - 298
3X-RAY DIFFRACTION1allC3 - 298
4X-RAY DIFFRACTION1allD4 - 298
5X-RAY DIFFRACTION1allG1
6X-RAY DIFFRACTION1allH1
7X-RAY DIFFRACTION1allS1 - 520
8X-RAY DIFFRACTION1allJ1
9X-RAY DIFFRACTION1allK1
10X-RAY DIFFRACTION1allL1
11X-RAY DIFFRACTION1allM1
12X-RAY DIFFRACTION1allN1
13X-RAY DIFFRACTION1allO1
14X-RAY DIFFRACTION1allP1
15X-RAY DIFFRACTION1allI1
16X-RAY DIFFRACTION1allQ1
17X-RAY DIFFRACTION1allR1
18X-RAY DIFFRACTION1allT1
19X-RAY DIFFRACTION1allU1
20X-RAY DIFFRACTION1allV1
21X-RAY DIFFRACTION1allE1
22X-RAY DIFFRACTION1allF1

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