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- PDB-6w1h: Crystal structure of the hydroxyglutarate synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6w1h
TitleCrystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida
ComponentsHydroxyglutarate synthase
KeywordsLYASE / Decarboxylase / Lysine catabolism
Function / homology
Function and homology information


2-oxoadipate dioxygenase/decarboxylase / dioxygenase activity
Similarity search - Function
Uncharacterised protein PF07063, DUF1338 / : / Domain of unknown function DUF1338 / 2-oxoadipate dioxygenase/decarboxylase / DUF1338 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / 2-OXOADIPIC ACID / 2-oxoadipate dioxygenase/decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsPereira, J.H. / Thompson, M.G. / Blake-Hedges, J.M. / Keasling, J.D. / Adams, P.D.
CitationJournal: Nat Commun / Year: 2020
Title: An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.
Authors: Thompson, M.G. / Blake-Hedges, J.M. / Pereira, J.H. / Hangasky, J.A. / Belcher, M.S. / Moore, W.M. / Barajas, J.F. / Cruz-Morales, P. / Washington, L.J. / Haushalter, R.W. / Eiben, C.B. / ...Authors: Thompson, M.G. / Blake-Hedges, J.M. / Pereira, J.H. / Hangasky, J.A. / Belcher, M.S. / Moore, W.M. / Barajas, J.F. / Cruz-Morales, P. / Washington, L.J. / Haushalter, R.W. / Eiben, C.B. / Liu, Y. / Skyrud, W. / Benites, V.T. / Barnum, T.P. / Baidoo, E.E.K. / Scheller, H.V. / Marletta, M.A. / Shih, P.M. / Adams, P.D. / Keasling, J.D.
History
DepositionMar 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6473
Polymers51,4281
Non-polymers2192
Water11,962664
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.442, 100.284, 103.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Hydroxyglutarate synthase


Mass: 51427.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ydcJ, PP_5260 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88CC1
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Fluoride, 20 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.42→72.05 Å / Num. obs: 593341 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 15.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 1.42→1.47 Å / Num. unique obs: 56327 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RJB

2rjb


Resolution: 1.42→72.05 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.2563
RfactorNum. reflection% reflection
Rfree0.1937 4041 4.8 %
Rwork0.1572 --
obs0.159 84228 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.42→72.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 12 664 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823657
X-RAY DIFFRACTIONf_angle_d0.86954968
X-RAY DIFFRACTIONf_chiral_restr0.2246549
X-RAY DIFFRACTIONf_plane_restr0.0063669
X-RAY DIFFRACTIONf_dihedral_angle_d20.52051373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.36451210.27382666X-RAY DIFFRACTION98.2
1.44-1.450.31261310.23472765X-RAY DIFFRACTION99.45
1.45-1.470.281250.22152741X-RAY DIFFRACTION99.69
1.47-1.490.26571300.21112693X-RAY DIFFRACTION99.54
1.49-1.510.26231260.19832754X-RAY DIFFRACTION99.86
1.51-1.530.25731270.19222751X-RAY DIFFRACTION99.83
1.53-1.560.22711270.18272739X-RAY DIFFRACTION99.83
1.56-1.580.24451410.17392737X-RAY DIFFRACTION99.93
1.58-1.610.2231520.17572690X-RAY DIFFRACTION99.96
1.61-1.630.24751400.17792774X-RAY DIFFRACTION99.9
1.63-1.660.22721380.16842717X-RAY DIFFRACTION99.96
1.66-1.70.26471320.16682778X-RAY DIFFRACTION99.86
1.7-1.730.21741450.16472719X-RAY DIFFRACTION99.93
1.73-1.770.20031410.15892757X-RAY DIFFRACTION99.97
1.77-1.810.18741190.15952752X-RAY DIFFRACTION100
1.81-1.850.19991300.15512787X-RAY DIFFRACTION99.9
1.85-1.90.21411540.1522717X-RAY DIFFRACTION99.86
1.9-1.960.17721590.15052734X-RAY DIFFRACTION100
1.96-2.020.18581550.1482754X-RAY DIFFRACTION99.97
2.02-2.10.18251340.13682763X-RAY DIFFRACTION100
2.1-2.180.18521530.13952755X-RAY DIFFRACTION99.97
2.18-2.280.14611680.13192749X-RAY DIFFRACTION99.97
2.28-2.40.15721330.13152796X-RAY DIFFRACTION100
2.4-2.550.16831460.13682765X-RAY DIFFRACTION100
2.55-2.750.16511410.14522815X-RAY DIFFRACTION100
2.75-3.020.18331650.15822800X-RAY DIFFRACTION99.97
3.02-3.460.19851320.15482823X-RAY DIFFRACTION100
3.46-4.360.18161440.15042880X-RAY DIFFRACTION100
4.36-72.050.20171320.17443016X-RAY DIFFRACTION99.71

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