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- PDB-5hwm: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -

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Basic information

Entry
Database: PDB / ID: 5hwm
TitleCrystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid
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 / 2-OXOADIPIC ACID / Probable 5-dehydro-4-deoxyglucarate dehydratase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.097 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
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)134,98210
Polymers134,2494
Non-polymers7336
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-63 kcal/mol
Surface area39250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.520, 119.030, 74.280
Angle α, β, γ (deg.)90.00, 112.24, 90.00
Int Tables number5
Space group name H-MC121

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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-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O5
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.39 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 12, 2013
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→47.9 Å / Num. obs: 76785 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIXdev_1803refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.097→47.883 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 3838 5 %Random selection
Rwork0.1987 ---
obs0.2027 76762 96.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.097→47.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 46 448 9638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159649
X-RAY DIFFRACTIONf_angle_d1.50913074
X-RAY DIFFRACTIONf_dihedral_angle_d15.2343520
X-RAY DIFFRACTIONf_chiral_restr0.0631440
X-RAY DIFFRACTIONf_plane_restr0.0081724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0965-2.1230.46031330.3572538X-RAY DIFFRACTION89
2.123-2.1510.39221400.33792648X-RAY DIFFRACTION96
2.151-2.18050.40431420.30852707X-RAY DIFFRACTION96
2.1805-2.21160.3591420.28882687X-RAY DIFFRACTION97
2.2116-2.24460.35731430.27062735X-RAY DIFFRACTION97
2.2446-2.27970.31341430.27222712X-RAY DIFFRACTION97
2.2797-2.31710.3441430.23672732X-RAY DIFFRACTION97
2.3171-2.3570.34861430.22712714X-RAY DIFFRACTION98
2.357-2.39990.2971450.20512742X-RAY DIFFRACTION98
2.3999-2.4460.28711430.2012722X-RAY DIFFRACTION98
2.446-2.4960.28551460.19072776X-RAY DIFFRACTION98
2.496-2.55020.2861440.18982746X-RAY DIFFRACTION98
2.5502-2.60950.29471440.20042728X-RAY DIFFRACTION97
2.6095-2.67480.31851440.20822742X-RAY DIFFRACTION97
2.6748-2.74710.32881430.2072715X-RAY DIFFRACTION97
2.7471-2.82790.30821400.21922650X-RAY DIFFRACTION95
2.8279-2.91920.30451210.21462311X-RAY DIFFRACTION83
2.9192-3.02350.26471430.19972707X-RAY DIFFRACTION96
3.0235-3.14460.28891460.19212782X-RAY DIFFRACTION98
3.1446-3.28760.24611450.19192746X-RAY DIFFRACTION98
3.2876-3.46090.27951470.18712795X-RAY DIFFRACTION98
3.4609-3.67770.26671440.1852731X-RAY DIFFRACTION98
3.6777-3.96150.27311470.18062795X-RAY DIFFRACTION98
3.9615-4.35990.2351440.1632747X-RAY DIFFRACTION97
4.3599-4.99030.22271420.15592695X-RAY DIFFRACTION96
4.9903-6.2850.22681310.17442483X-RAY DIFFRACTION88
6.285-47.89540.21131500.18272838X-RAY DIFFRACTION98

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