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- PDB-4m19: dihydrodipicolinate synthase from C. jejuni with pyruvate bound t... -

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Basic information

Entry
Database: PDB / ID: 4m19
Titledihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site and Lysine bound to allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / schiff-base / aldolase / TIM barrel
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / 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
LYSINE / DI(HYDROXYETHYL)ETHER / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciescampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsConly, C.J.T.
CitationJournal: Biochemistry / Year: 2014
Title: Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine.
Authors: Conly, C.J. / Skovpen, Y.V. / Li, S. / Palmer, D.R. / Sanders, D.A.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,08012
Polymers135,0674
Non-polymers1,0138
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-54 kcal/mol
Surface area39590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.640, 96.990, 79.560
Angle α, β, γ (deg.)90.00, 111.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)
21chain D and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)
12chain B and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)
22chain C and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNVALVALchain A and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)AA4 - 16512 - 173
121GLUGLUPHEPHEchain A and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)AA167 - 298175 - 306
211ASNASNVALVALchain D and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)DD4 - 16512 - 173
221GLUGLUPHEPHEchain D and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)DD167 - 298175 - 306
112ASNASNVALVALchain B and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)BB4 - 16512 - 173
122GLUGLUPHEPHEchain B and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)BB167 - 298175 - 306
212ASNASNVALVALchain C and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)CC4 - 16512 - 173
222GLUGLUPHEPHEchain C and (resseq 4:165 or resseq 167:298 ) and (not element H) and (not element D)CC167 - 298175 - 306

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 33766.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0806, 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, 531 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 288 K / Method: hanging drop / pH: 8.5
Details: 35% PEG3350, 0.3 M NH4SO4, 0.1 mM TRIS, pH 8.5, hanging drop, temperature 288K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 12, 2012
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. all: 93713 / Num. obs: 93713 / % possible obs: 78.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.24 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.82
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.71-1.820.8617568649833.9
1.82-1.941.6829487927951.5
1.94-2.13.27476081337379.8
2.1-2.35.51584821527998.6
2.3-2.578.68537201387899
2.57-2.9713.82475881231099.4
2.97-3.6325.7402691042099.4
3.63-5.1244.431226810299.5
5.1249.8617269457499.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2→48.495 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.881 / SU ML: 0.52 / σ(F): 2 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 3668 5 %random
Rwork0.165 ---
all0.1671 73351 --
obs0.1671 73351 97.72 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.063 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 24.095 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1-6.8609 Å2-0 Å23.4359 Å2
2---1.8996 Å20 Å2
3----4.9613 Å2
Refinement stepCycle: LAST / Resolution: 2→48.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9089 0 68 523 9680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069377
X-RAY DIFFRACTIONf_angle_d1.03212677
X-RAY DIFFRACTIONf_chiral_restr0.0891471
X-RAY DIFFRACTIONf_plane_restr0.0051625
X-RAY DIFFRACTIONf_dihedral_angle_d14.2463551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2233X-RAY DIFFRACTIONTORSIONAL0.402
12D2233X-RAY DIFFRACTIONTORSIONAL0.402
21B2234X-RAY DIFFRACTIONTORSIONAL0.547
22C2234X-RAY DIFFRACTIONTORSIONAL0.547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02620.30721110.21832108221976
2.0262-2.0540.24331240.20382357248186
2.054-2.08330.25021360.19482586272296
2.0833-2.11440.24291420.19332693283598
2.1144-2.14750.2491410.18152681282299
2.1475-2.18270.23951420.18382707284999
2.1827-2.22030.23281410.17442679282098
2.2203-2.26070.25631420.19382691283398
2.2607-2.30420.22341430.15332717286099
2.3042-2.35120.19121430.15462720286399
2.3512-2.40230.20261430.15542707285099
2.4023-2.45820.23971420.16232710285299
2.4582-2.51970.21111420.16422687282999
2.5197-2.58780.21371420.15772711285399
2.5878-2.6640.20991450.16012748289399
2.664-2.74990.19661430.1612716285999
2.7499-2.84820.22411450.16362747289299
2.8482-2.96220.2061420.167827122854100
2.9622-3.0970.21741430.166727112854100
3.097-3.26030.19141440.1727342878100
3.2603-3.46450.2341450.16227602905100
3.4645-3.73190.16851440.156127312875100
3.7319-4.10730.16591440.153827372881100
4.1073-4.70120.17011450.145927582903100
4.7012-5.92130.18691460.167727732919100
5.9213-48.50920.1881480.16462802295099

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