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- PDB-8gek: Dihydrodipicolinate synthase with pyruvate from Candidatus Liberi... -

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Basic information

Entry
Database: PDB / ID: 8gek
TitleDihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / TIM Barrel
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / L-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
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCandidatus Liberibacter solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum
Authors: Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)192,2296
Polymers192,2296
Non-polymers00
Water17,457969
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase

A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)128,1534
Polymers128,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9520 Å2
ΔGint-59 kcal/mol
Surface area39240 Å2
MethodPISA
2
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase


Theoretical massNumber of molelcules
Total (without water)128,1534
Polymers128,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-58 kcal/mol
Surface area39170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.112, 132.920, 154.904
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase


Mass: 32038.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter solanacearum (bacteria)
Gene: dapA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F4VK59
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallization trials used the sitting drop vapour diffusion method, at 20 C, with droplets consisting of 150 nL of protein solution and 150 nL of reservoir solution. Rectangular CLsoDHDPS ...Details: Crystallization trials used the sitting drop vapour diffusion method, at 20 C, with droplets consisting of 150 nL of protein solution and 150 nL of reservoir solution. Rectangular CLsoDHDPS crystals were produced using the JCSG+ Suite screen in condition A2 (20% w/v polyethylene glycol 3000, 0.1 M sodium citrate, pH 5.5). For ligand bound structures, the crystals were soaked for 7 days in mother liquor with either: 100 mM lysine, 100 mM pyruvate or 100 mM of both succinic semi-aldehyde and pyruvate.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→45.81 Å / Num. obs: 151510 / % possible obs: 99.5 % / Redundancy: 3.94 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.8
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 6831 / CC1/2: 0.468

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→45.81 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 4544 3 %
Rwork0.1851 --
obs0.1864 151353 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13476 0 0 969 14445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071
X-RAY DIFFRACTIONf_angle_d0.9681
X-RAY DIFFRACTIONf_dihedral_angle_d6.8841934
X-RAY DIFFRACTIONf_chiral_restr0.2412162
X-RAY DIFFRACTIONf_plane_restr0.0062426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.42991460.39974245X-RAY DIFFRACTION87
1.95-1.970.35321660.34744817X-RAY DIFFRACTION100
1.97-1.990.35351380.33864944X-RAY DIFFRACTION100
1.99-2.020.32441230.30764949X-RAY DIFFRACTION100
2.02-2.050.34391570.3014872X-RAY DIFFRACTION100
2.05-2.070.33911380.28884888X-RAY DIFFRACTION100
2.07-2.10.30111450.26044925X-RAY DIFFRACTION100
2.1-2.130.26651450.24784917X-RAY DIFFRACTION100
2.13-2.170.28621460.2494860X-RAY DIFFRACTION100
2.17-2.20.28871580.23554929X-RAY DIFFRACTION100
2.2-2.240.27761530.23184941X-RAY DIFFRACTION100
2.24-2.280.2591480.21594846X-RAY DIFFRACTION100
2.28-2.330.25641580.20024915X-RAY DIFFRACTION100
2.33-2.370.24461610.19484918X-RAY DIFFRACTION100
2.37-2.430.23771600.19014877X-RAY DIFFRACTION100
2.43-2.480.23361490.18674906X-RAY DIFFRACTION100
2.48-2.540.22491290.18354973X-RAY DIFFRACTION100
2.54-2.610.24421610.18794893X-RAY DIFFRACTION100
2.61-2.690.2551440.18524907X-RAY DIFFRACTION100
2.69-2.780.2121710.18114908X-RAY DIFFRACTION100
2.78-2.880.25541570.18124923X-RAY DIFFRACTION100
2.88-2.990.26411520.19294921X-RAY DIFFRACTION100
2.99-3.130.25021370.19644907X-RAY DIFFRACTION100
3.13-3.290.24411430.19984910X-RAY DIFFRACTION100
3.29-3.50.22951520.17534962X-RAY DIFFRACTION100
3.5-3.770.19981370.16214934X-RAY DIFFRACTION100
3.77-4.150.18491720.1434927X-RAY DIFFRACTION100
4.15-4.750.15411530.12314939X-RAY DIFFRACTION100
4.75-5.980.15241700.14374977X-RAY DIFFRACTION100
5.98-45.810.18491750.15574979X-RAY DIFFRACTION100

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