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- PDB-4ur7: Crystal structure of keto-deoxy-D-galactarate dehydratase complex... -

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Basic information

Entry
Database: PDB / ID: 4ur7
TitleCrystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate
ComponentsKETO-DEOXY-D-GALACTARATE DEHYDRATASE
KeywordsLYASE / DECARBOXYLATE / BIOCATALYSIS / OXIDATIVE PATHWAY / D-GALACTURONIC ACID
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 TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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.B. / Parkkinen, T. / Janis, J. / Penttila, M. / Hakulinen, N. / Koivula, A. / Rouvinen, J.
History
DepositionJun 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
B: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
C: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
D: KETO-DEOXY-D-GALACTARATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,63118
Polymers134,5264
Non-polymers1,10514
Water28,0851559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-38.7 kcal/mol
Surface area40360 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-2092-

HOH

21D-2063-

HOH

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Components

#1: Protein
KETO-DEOXY-D-GALACTARATE DEHYDRATASE / KDGDH / 5-KETO-4-DEOXY-GLUCARATE DEHYDRATASE


Mass: 33631.402 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Plasmid: PBAT4-ATKDG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: Q8UB77, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 1559 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 8.5 / Details: BICINE PH 8.5, SODIUM FORMATE, PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 214991 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.64
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.27 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UR5

4ur5
PDB Unreleased entry


Resolution: 1.499→48.087 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 10750 5 %
Rwork0.1627 --
obs0.1637 214967 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.68 Å2
Refinement stepCycle: LAST / Resolution: 1.499→48.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9289 0 72 1559 10920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069604
X-RAY DIFFRACTIONf_angle_d1.07812994
X-RAY DIFFRACTIONf_dihedral_angle_d13.433479
X-RAY DIFFRACTIONf_chiral_restr0.0451434
X-RAY DIFFRACTIONf_plane_restr0.0061694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.51610.29933500.29096650X-RAY DIFFRACTION96
1.5161-1.53390.26923600.24936831X-RAY DIFFRACTION99
1.5339-1.55260.25653620.23726886X-RAY DIFFRACTION99
1.5526-1.57230.25713610.22716848X-RAY DIFFRACTION99
1.5723-1.59290.25543610.21646863X-RAY DIFFRACTION99
1.5929-1.61480.25493600.21456830X-RAY DIFFRACTION99
1.6148-1.63780.23843580.21456814X-RAY DIFFRACTION99
1.6378-1.66230.2313640.20066912X-RAY DIFFRACTION99
1.6623-1.68830.2043620.19076885X-RAY DIFFRACTION99
1.6883-1.71590.22433620.19266866X-RAY DIFFRACTION99
1.7159-1.74550.20363600.18486836X-RAY DIFFRACTION99
1.7455-1.77730.20293590.18566823X-RAY DIFFRACTION99
1.7773-1.81150.19633630.17386896X-RAY DIFFRACTION99
1.8115-1.84840.20363620.17226874X-RAY DIFFRACTION99
1.8484-1.88860.1833600.16956842X-RAY DIFFRACTION98
1.8886-1.93260.21893590.17746819X-RAY DIFFRACTION98
1.9326-1.98090.19813570.17196783X-RAY DIFFRACTION98
1.9809-2.03450.18043630.176892X-RAY DIFFRACTION98
2.0345-2.09430.19953560.17026781X-RAY DIFFRACTION98
2.0943-2.16190.19713600.17396839X-RAY DIFFRACTION98
2.1619-2.23920.20793570.16746785X-RAY DIFFRACTION97
2.2392-2.32880.18683540.16426716X-RAY DIFFRACTION97
2.3288-2.43480.17423550.16426746X-RAY DIFFRACTION97
2.4348-2.56320.1843570.1616774X-RAY DIFFRACTION97
2.5632-2.72380.17573560.15956765X-RAY DIFFRACTION97
2.7238-2.93410.17733530.15966718X-RAY DIFFRACTION96
2.9341-3.22930.16133530.15416713X-RAY DIFFRACTION96
3.2293-3.69640.1473520.1436674X-RAY DIFFRACTION95
3.6964-4.65650.14263540.12896727X-RAY DIFFRACTION96
4.6565-48.11180.17163600.14436829X-RAY DIFFRACTION96

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