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- PDB-3fkr: Structure of L-2-keto-3-deoxyarabonate dehydratase complex with p... -

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Basic information

Entry
Database: PDB / ID: 3fkr
TitleStructure of L-2-keto-3-deoxyarabonate dehydratase complex with pyruvate
ComponentsL-2-keto-3-deoxyarabonate dehydratase
KeywordsLYASE / DHDPS/NAL family / complex / pyruvate
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 / protein homodimerization activity
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 / Resolution: 1.801 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 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)68,41211
Polymers67,7012
Non-polymers7119
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-21 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.259, 79.259, 206.527
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-1109-

HOH

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Components

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


Mass: 33850.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JUQ0
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.77 Å3/Da / Density % sol: 55.53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70047 / % possible obs: 99.5 % / Biso Wilson estimate: 19.99 Å2
Reflection shellResolution: 1.8→1.86 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
PROCESSdata scaling
RefinementResolution: 1.801→14.997 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.23 / σ(F): 1.33 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 3519 5.04 %
Rwork0.1956 --
obs0.1977 69759 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.641 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 86.39 Å2 / Biso mean: 22.643 Å2 / Biso min: 4.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.108 Å20 Å20 Å2
2--3.108 Å20 Å2
3----6.216 Å2
Refinement stepCycle: LAST / Resolution: 1.801→14.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 37 602 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0254959
X-RAY DIFFRACTIONf_angle_d2.0476777
X-RAY DIFFRACTIONf_chiral_restr0.138747
X-RAY DIFFRACTIONf_plane_restr0.01901
X-RAY DIFFRACTIONf_dihedral_angle_d19.131851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.8260.26721490.19632431X-RAY DIFFRACTION93
1.826-1.8520.26781400.18662641X-RAY DIFFRACTION100
1.852-1.87960.24521470.18272625X-RAY DIFFRACTION100
1.8796-1.90890.25221340.18452640X-RAY DIFFRACTION100
1.9089-1.94020.23731220.17632666X-RAY DIFFRACTION100
1.9402-1.97360.2361250.17582645X-RAY DIFFRACTION100
1.9736-2.00940.21961590.17442585X-RAY DIFFRACTION100
2.0094-2.04790.22931310.1712680X-RAY DIFFRACTION100
2.0479-2.08960.23131310.17412658X-RAY DIFFRACTION100
2.0896-2.13490.24051390.16572655X-RAY DIFFRACTION100
2.1349-2.18440.22811390.17322630X-RAY DIFFRACTION100
2.1844-2.23890.22741400.16892617X-RAY DIFFRACTION100
2.2389-2.29920.21481500.1732667X-RAY DIFFRACTION100
2.2992-2.36660.25241460.17622651X-RAY DIFFRACTION100
2.3666-2.44270.19771220.18162655X-RAY DIFFRACTION100
2.4427-2.52960.23771530.1792648X-RAY DIFFRACTION100
2.5296-2.63040.21271460.17412682X-RAY DIFFRACTION100
2.6304-2.74940.20581280.19072671X-RAY DIFFRACTION100
2.7494-2.89340.25881530.20272634X-RAY DIFFRACTION100
2.8934-3.07320.2271630.20452678X-RAY DIFFRACTION100
3.0732-3.30810.24071270.19742702X-RAY DIFFRACTION99
3.3081-3.63670.22951300.20032684X-RAY DIFFRACTION99
3.6367-4.15320.23161420.20332669X-RAY DIFFRACTION98
4.1532-5.19610.22581510.20282601X-RAY DIFFRACTION95
5.1961-14.99790.2471520.23142825X-RAY DIFFRACTION98

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