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- PDB-3uqn: Crystal structure of dihydrodipicolinate synthase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 3uqn
TitleCrystal structure of dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Oxamic acid at 1.9 Angstrom resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / TIM Barrel / Lysine biosynthesis / Oxamic acid
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 / metal ion binding / 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
OXAMIC ACID / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSingh, A. / Kaushik, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Oxamic acid at 1.9 Angstrom resolution
Authors: Singh, A. / Kaushik, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)62,9226
Polymers62,5602
Non-polymers3624
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-11 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.374, 122.637, 52.332
Angle α, β, γ (deg.)90.00, 115.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrodipicolinate synthase


Mass: 31279.842 Da / Num. of mol.: 2 / Fragment: UNP residues 7-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: dhdps, HMPREF0010_03414 / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: D0CFC3, dihydrodipicolinate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MgCl2, PEG3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2011 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.94→61.32 Å / Num. all: 45562 / Num. obs: 45562 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.101 / Net I/σ(I): 8.8
Reflection shellResolution: 1.94→2.01 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.308 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RK8

3rk8


Resolution: 1.94→61.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19836 2167 5 %RANDOM
Rwork0.17899 ---
obs0.17995 40876 99.64 %-
all-45562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.7 Å2
2---0.36 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.94→61.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 24 624 5036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg1.539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.001
X-RAY DIFFRACTIONr_chiral_restr0.104
X-RAY DIFFRACTIONr_gen_planes_refined0.008
X-RAY DIFFRACTIONr_mcbond_it1.279
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 178 -
Rwork0.311 3014 -
obs--99.97 %

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