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- PDB-4mlj: dihydrodipicolinate synthase from C. jejuni, Y110F mutation with ... -

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Basic information

Entry
Database: PDB / ID: 4mlj
Titledihydrodipicolinate synthase from C. jejuni, Y110F mutation with pyruvate bound to the active site
Componentsdihydrodipicolinate synthase
KeywordsLYASE / schiff-base / aldolase / TIM barrel
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
TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Data collection
Revision 1.2Apr 1, 2015Group: Structure summary
Revision 1.3Sep 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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: dihydrodipicolinate synthase
B: dihydrodipicolinate synthase
C: dihydrodipicolinate synthase
D: dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5048
Polymers134,9474
Non-polymers5574
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-46 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.610, 97.240, 148.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33736.746 Da / Num. of mol.: 4 / Mutation: Y110F
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
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% PEG4000, 0.2 M sodium acetate, 0.1 mM TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-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: 1.41→50 Å / Num. obs: 52574 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.43 / Net I/σ(I): 4.21
Reflection shell

Rmerge(I) obs: 0.09 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.41-1.50.0914267717520
1.5-1.60.2545721961858
1.6-1.730.341061562827689.7
1.73-1.890.8519147129020100
1.89-2.112.0721854626368100
2.11-2.444.2319324323314100
2.44-2.997.1216498719796100
2.99-4.2214.5212690715496100
4.2221.769156884999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXdev_1356refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.3→48.62 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8924 / SU ML: 0.23 / σ(F): 2.01 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2629 5 %random
Rwork0.1408 ---
all0.1438 52571 --
obs0.1438 52571 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.89 Å2 / Biso mean: 20.1662 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9135 0 37 483 9655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079342
X-RAY DIFFRACTIONf_angle_d1.07912616
X-RAY DIFFRACTIONf_chiral_restr0.0721457
X-RAY DIFFRACTIONf_plane_restr0.0051614
X-RAY DIFFRACTIONf_dihedral_angle_d13.6743524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.34170.25751350.165425672702
2.3417-2.38680.2391370.15126052742
2.3868-2.43550.24061370.152626042741
2.4355-2.48840.23561350.1425532688
2.4884-2.54630.18861370.137826122749
2.5463-2.610.21171380.131626152753
2.61-2.68060.22251360.132925962732
2.6806-2.75940.21591370.139925892726
2.7594-2.84850.22761370.144926152752
2.8485-2.95030.23511380.148226162754
2.9503-3.06840.23131370.148425972734
3.0684-3.2080.20591380.149326232761
3.208-3.37710.2021390.147326442783
3.3771-3.58860.21281380.141926192757
3.5886-3.86560.17021380.135126352773
3.8656-4.25440.17251400.119626552795
4.2544-4.86950.15481410.125326762817
4.8695-6.13320.1871420.14726982840
6.1332-48.63080.17021490.149728232972
Refinement TLS params.Method: refined / Origin x: 46.2365 Å / Origin y: 3.3323 Å / Origin z: 18.532 Å
111213212223313233
T0.0979 Å2-0.0074 Å2-0.0027 Å2-0.0805 Å20.0037 Å2--0.0925 Å2
L0.192 °2-0.0404 °2-0 °2-0.109 °20.0301 °2--0.1555 °2
S-0.007 Å °-0.0024 Å °0.0113 Å °-0.0082 Å °-0.0011 Å °-0.0016 Å °-0.0128 Å °0.0122 Å °0.0052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 298
2X-RAY DIFFRACTION1allB1 - 298
3X-RAY DIFFRACTION1allC2 - 298
4X-RAY DIFFRACTION1allD2 - 298
5X-RAY DIFFRACTION1allD1 - 301
6X-RAY DIFFRACTION1allA1 - 301
7X-RAY DIFFRACTION1allC1 - 301
8X-RAY DIFFRACTION1allC1 - 302
9X-RAY DIFFRACTION1allC - A1 - 571

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