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- PDB-3u8g: Crystal structure of the complex of Dihydrodipicolinate synthase ... -

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Basic information

Entry
Database: PDB / ID: 3u8g
TitleCrystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with Oxalic acid at 1.80 A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / DHDPS / Lysine biosynthesis / Oxalic acid / TIM Barrel
Function / homology
Function and homology information


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
OXALATE ION / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, M. / Kaushik, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with Oxalic acid at 1.80 A resolution
Authors: Kumar, M. / Kaushik, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 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)62,7364
Polymers62,5602
Non-polymers1762
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-10 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.372, 122.436, 51.344
Angle α, β, γ (deg.)90.00, 115.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrodipicolinate synthase / / DHDPS


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: pRESTa / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: D0CFC3, dihydrodipicolinate synthase
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M MgCl2, PEG 3350, pH 6.2, 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 22, 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: 1.8→61.2 Å / Num. all: 51034 / Num. obs: 51034 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.098 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.448 / % possible all: 100

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Processing

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

3rk8


Resolution: 1.8→47.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.349 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21159 2726 5.1 %RANDOM
Rwork0.1744 ---
all0.17629 51034 --
obs0.17629 51034 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.857 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.26 Å2
2---0.57 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 12 621 5023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224468
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.986082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8225.93172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0561518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213292
X-RAY DIFFRACTIONr_mcbond_it0.7361.52894
X-RAY DIFFRACTIONr_mcangle_it1.37924672
X-RAY DIFFRACTIONr_scbond_it2.67231574
X-RAY DIFFRACTIONr_scangle_it4.3094.51410
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 212 -
Rwork0.247 3698 -
obs--98.64 %

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