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- PDB-5hwj: Crystal structure of keto-deoxy-D-galactarate dehydratase -

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Basic information

Entry
Database: PDB / ID: 5hwj
TitleCrystal structure of keto-deoxy-D-galactarate dehydratase
ComponentsProbable 5-dehydro-4-deoxyglucarate dehydratase
KeywordsLYASE / decarboxylating / dehydratase / TIM-barrel
Function / homology
Function and homology information


5-dehydro-4-deoxyglucarate dehydratase / 5-dehydro-4-deoxyglucarate dehydratase activity / D-glucarate catabolic process / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
5-dehydro-4-deoxyglucarate dehydratase / 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
FORMIC ACID / Probable 5-dehydro-4-deoxyglucarate dehydratase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.648 Å
AuthorsTaberman, H. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase.
Authors: Taberman, H. / Andberg, M. / Parkkinen, T. / Janis, J. / Penttila, M. / Hakulinen, N. / Koivula, A. / Rouvinen, J.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
SupersessionMar 30, 2016ID: 4UR5
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 5-dehydro-4-deoxyglucarate dehydratase
B: Probable 5-dehydro-4-deoxyglucarate dehydratase
C: Probable 5-dehydro-4-deoxyglucarate dehydratase
D: Probable 5-dehydro-4-deoxyglucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,03214
Polymers134,2494
Non-polymers78310
Water16,250902
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-64 kcal/mol
Surface area40060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.940, 118.420, 74.300
Angle α, β, γ (deg.)90.00, 112.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-787-

HOH

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Components

#1: Protein
Probable 5-dehydro-4-deoxyglucarate dehydratase / 5-keto-4-deoxy-glucarate dehydratase / KDGDH


Mass: 33562.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: Atu3140, AGR_L_3338 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8UB77, 5-dehydro-4-deoxyglucarate dehydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: BICINE, sodium formate, PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014
RadiationMonochromator: CHANNEL-CUT SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.65→47.7 Å / Num. obs: 159523 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIXdev_1803refinement
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+96 / Resolution: 1.648→47.709 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 7975 5 %Random selection
Rwork0.1607 ---
obs0.1622 159492 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.648→47.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 51 902 10169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019759
X-RAY DIFFRACTIONf_angle_d1.29813253
X-RAY DIFFRACTIONf_dihedral_angle_d13.9093577
X-RAY DIFFRACTIONf_chiral_restr0.0531468
X-RAY DIFFRACTIONf_plane_restr0.0081732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6483-1.6670.37662380.33664528X-RAY DIFFRACTION88
1.667-1.68670.33052600.29564953X-RAY DIFFRACTION97
1.6867-1.70720.31582610.2774978X-RAY DIFFRACTION98
1.7072-1.72880.2832660.2565048X-RAY DIFFRACTION97
1.7288-1.75160.25582660.24055039X-RAY DIFFRACTION99
1.7516-1.77560.29052640.22795016X-RAY DIFFRACTION97
1.7756-1.8010.24972630.21385001X-RAY DIFFRACTION98
1.801-1.82780.23282600.20734951X-RAY DIFFRACTION97
1.8278-1.85640.23862680.20315075X-RAY DIFFRACTION98
1.8564-1.88680.24292650.19015041X-RAY DIFFRACTION99
1.8868-1.91940.23362680.19185063X-RAY DIFFRACTION98
1.9194-1.95430.23532650.18725042X-RAY DIFFRACTION98
1.9543-1.99190.23822620.19085010X-RAY DIFFRACTION98
1.9919-2.03250.21242680.17265088X-RAY DIFFRACTION99
2.0325-2.07670.19922670.16585060X-RAY DIFFRACTION99
2.0767-2.1250.21722700.16945106X-RAY DIFFRACTION99
2.125-2.17820.21052670.1645108X-RAY DIFFRACTION99
2.1782-2.23710.19472690.1645104X-RAY DIFFRACTION99
2.2371-2.30290.19962640.15565009X-RAY DIFFRACTION98
2.3029-2.37720.17862680.15145102X-RAY DIFFRACTION99
2.3772-2.46220.19322690.15035101X-RAY DIFFRACTION99
2.4622-2.56080.19272670.15015086X-RAY DIFFRACTION99
2.5608-2.67730.1832710.14795124X-RAY DIFFRACTION99
2.6773-2.81840.21242690.15235116X-RAY DIFFRACTION99
2.8184-2.9950.16982680.16035093X-RAY DIFFRACTION99
2.995-3.22620.20262700.16735133X-RAY DIFFRACTION99
3.2262-3.55070.16872680.1565085X-RAY DIFFRACTION98
3.5507-4.06430.15712690.14285116X-RAY DIFFRACTION99
4.0643-5.11970.1292710.11455141X-RAY DIFFRACTION99
5.1197-47.72940.16652740.14635200X-RAY DIFFRACTION99

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