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- PDB-3fkk: Structure of L-2-keto-3-deoxyarabonate dehydratase -

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Basic information

Entry
Database: PDB / ID: 3fkk
TitleStructure of L-2-keto-3-deoxyarabonate dehydratase
ComponentsL-2-keto-3-deoxyarabonate dehydratase
KeywordsLYASE / DHDPS/NAL family
Function / homology
Function and homology information


2-dehydro-3-deoxy-L-arabinonate dehydratase / 2-dehydro-3-deoxy-L-arabinonate dehydratase activity / L-arabinose catabolic process to 2-oxoglutarate / 4-hydroxy-tetrahydrodipicolinate synthase activity / protein homodimerization activity / cytosol
Similarity search - Function
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
PHOSPHATE ION / L-2-keto-3-deoxyarabonate dehydratase
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsShimada, N. / Mikami, B.
CitationJournal: To be Published
Title: Structural analysis of L -2-keto-3-deoxyarabonate dehydratase an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism in complex with pyruvate
Authors: Shimada, N. / Mikami, B. / Watanabe, S. / Kodaki, T. / Makino, K.
History
DepositionDec 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: L-2-keto-3-deoxyarabonate dehydratase
B: L-2-keto-3-deoxyarabonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7534
Polymers67,5632
Non-polymers1902
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-20 kcal/mol
Surface area22340 Å2
MethodPISA
2
A: L-2-keto-3-deoxyarabonate dehydratase
B: L-2-keto-3-deoxyarabonate dehydratase
hetero molecules

A: L-2-keto-3-deoxyarabonate dehydratase
B: L-2-keto-3-deoxyarabonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5068
Polymers135,1264
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area11020 Å2
ΔGint-40 kcal/mol
Surface area39750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.911, 78.911, 207.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-655-

HOH

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Components

#1: Protein L-2-keto-3-deoxyarabonate dehydratase


Mass: 33781.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: AraD / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JUQ0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM Tris-HCl,5% 2-propanol, 0.4M Ammonium phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Iodine / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.8 Å / Num. obs: 48899 / % possible obs: 94.6 % / Observed criterion σ(I): 29.2 / Biso Wilson estimate: 10.1 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4173414.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4430 10.2 %RANDOM
Rwork0.184 ---
obs0.184 43627 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5829 Å2 / ksol: 0.392056 e/Å3
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.32 Å20 Å2
2--2.07 Å20 Å2
3----4.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 10 445 5137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 659 10.2 %
Rwork0.185 5824 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4carbohydrate.param

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