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

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Basic information

Entry
Database: PDB / ID: 5hwn
TitleCrystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate
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 / PYRUVIC ACID / Probable 5-dehydro-4-deoxyglucarate dehydratase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.499 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)135,89124
Polymers134,2494
Non-polymers1,64120
Water25,4011410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-44 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.800, 120.140, 74.070
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-892-

HOH

21D-822-

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-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 1410 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
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: I03 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→48.09 Å / Num. obs: 214991 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIXdev_1803refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.499→48.087 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1695 10750 5 %
Rwork0.1444 --
obs0.1456 214963 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→48.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9233 0 104 1410 10747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110280
X-RAY DIFFRACTIONf_angle_d1.30113997
X-RAY DIFFRACTIONf_dihedral_angle_d13.8523819
X-RAY DIFFRACTIONf_chiral_restr0.0791517
X-RAY DIFFRACTIONf_plane_restr0.0071858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.51610.31043500.29866650X-RAY DIFFRACTION96
1.5161-1.53390.26813600.24966831X-RAY DIFFRACTION99
1.5339-1.55260.25553620.23356886X-RAY DIFFRACTION99
1.5526-1.57230.25653610.22116848X-RAY DIFFRACTION99
1.5723-1.59290.25543610.20776863X-RAY DIFFRACTION99
1.5929-1.61480.25033600.20426830X-RAY DIFFRACTION99
1.6148-1.63780.22953580.20066814X-RAY DIFFRACTION99
1.6378-1.66230.21123640.18456912X-RAY DIFFRACTION99
1.6623-1.68830.18873620.17356885X-RAY DIFFRACTION99
1.6883-1.71590.21563620.17626866X-RAY DIFFRACTION99
1.7159-1.74550.19023600.16936836X-RAY DIFFRACTION99
1.7455-1.77730.18793590.16786823X-RAY DIFFRACTION99
1.7773-1.81150.20133630.15936896X-RAY DIFFRACTION99
1.8115-1.84840.19463620.15826874X-RAY DIFFRACTION99
1.8484-1.88860.18583600.15556842X-RAY DIFFRACTION98
1.8886-1.93260.20513590.16096819X-RAY DIFFRACTION98
1.9326-1.98090.18673570.15426783X-RAY DIFFRACTION98
1.9809-2.03450.16873630.15096892X-RAY DIFFRACTION98
2.0345-2.09430.17993560.14956781X-RAY DIFFRACTION98
2.0943-2.16190.18513600.14986839X-RAY DIFFRACTION98
2.1619-2.23920.18363570.14236785X-RAY DIFFRACTION97
2.2392-2.32880.16353540.13736716X-RAY DIFFRACTION97
2.3288-2.43480.15553550.13426746X-RAY DIFFRACTION97
2.4348-2.56320.16213570.1296774X-RAY DIFFRACTION97
2.5632-2.72380.15813560.13026765X-RAY DIFFRACTION97
2.7238-2.93410.15773530.13396718X-RAY DIFFRACTION96
2.9341-3.22930.15033530.13396713X-RAY DIFFRACTION96
3.2293-3.69640.13613520.1316674X-RAY DIFFRACTION95
3.6964-4.65650.14133540.11516727X-RAY DIFFRACTION96
4.6565-48.11180.15453600.13346825X-RAY DIFFRACTION96

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