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- PDB-4i7w: Agrobacterium tumefaciens DHDPS with lysine and pyruvate -

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Basic information

Entry
Database: PDB / ID: 4i7w
TitleAgrobacterium tumefaciens DHDPS with lysine and pyruvate
ComponentsDihydrodipicolinate synthase
KeywordsBIOSYNTHETIC PROTEIN / TIM BARREL / lysine biosynthesis / pyruvate bound to acitve site lysine / cytosol
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
LYSINE / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAgrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAtkinson, S.C. / Dogovski, C. / Dobson, R.C.J. / Perugini, M.A.
CitationJournal: To be Published
Title: Structure, function and allostery of the bona fide DHDPS from the plant pathogen Agrobacterium tumefaciens
Authors: Atkinson, S.C. / Dogovski, C. / Dobson, R.C.J. / Perugini, M.A.
History
DepositionDec 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3385
Polymers65,9512
Non-polymers3863
Water15,835879
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,67510
Polymers131,9024
Non-polymers7736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10220 Å2
ΔGint-56 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.090, 122.780, 129.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dihydrodipicolinate synthase / DHDPS


Mass: 32975.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium sp. (bacteria) / Strain: H13-3 / Gene: dapA, AGROH133_05014 / Production host: Escherichia coli (E. coli) / References: UniProt: F0L8Z6, dihydrodipicolinate synthase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER190 AND CYS263 ARE CONSISTENT WITH BOTH DNA SEQUENCING AND THE CRYSTAL STRUCTURE

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M lithium sulfate monohydrate, 0.085 M Tris pH 8.5, 25.5 % (w/v) PEG 4000, 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.3→40 Å / Num. obs: 39292 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.695 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18647 2340 1.5 %RANDOM
Rwork0.1717 ---
obs0.17192 -90.07 %-
all-457924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 26 879 5255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9736526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1815672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57824.776201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57915796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4051526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2841.53074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55124974
X-RAY DIFFRACTIONr_scbond_it0.92731687
X-RAY DIFFRACTIONr_scangle_it1.5794.51508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 103 -
Rwork0.307 6538 -
obs--51.96 %

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