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- PDB-6w1g: Crystal structure of the hydroxyglutarate synthase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 6w1g
TitleCrystal structure of the hydroxyglutarate synthase 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-oxoadipate dioxygenase/decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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)51,4862
Polymers51,4281
Non-polymers591
Water11,782654
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.449, 100.746, 104.765
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: isolated from a natural source / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
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: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→52.38 Å / Num. obs: 164046 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 13 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.3
Reflection shellResolution: 1.14→1.18 Å / Num. unique obs: 16167 / CC1/2: 0.666

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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: 1.14→52.38 Å / SU ML: 0.1029 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 14.7214
RfactorNum. reflection% reflection
Rfree0.166 8263 5.04 %
Rwork0.1423 --
obs0.1435 164046 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.97 Å2
Refinement stepCycle: LAST / Resolution: 1.14→52.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 1 654 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01223545
X-RAY DIFFRACTIONf_angle_d1.22524826
X-RAY DIFFRACTIONf_chiral_restr0.1842540
X-RAY DIFFRACTIONf_plane_restr0.0089647
X-RAY DIFFRACTIONf_dihedral_angle_d18.19881332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.27652890.26055054X-RAY DIFFRACTION97.45
1.15-1.170.26092550.23655077X-RAY DIFFRACTION99.98
1.17-1.180.27652560.22525200X-RAY DIFFRACTION100
1.18-1.20.22372490.21775129X-RAY DIFFRACTION100
1.2-1.210.23552890.2065197X-RAY DIFFRACTION100
1.21-1.230.22372630.2055103X-RAY DIFFRACTION100
1.23-1.250.20542710.19415163X-RAY DIFFRACTION100
1.25-1.260.22492490.1865157X-RAY DIFFRACTION99.94
1.26-1.280.22830.17595182X-RAY DIFFRACTION100
1.28-1.30.20222740.18465108X-RAY DIFFRACTION100
1.3-1.330.18632910.15695174X-RAY DIFFRACTION100
1.33-1.350.17542460.15295158X-RAY DIFFRACTION100
1.35-1.380.19492930.14595150X-RAY DIFFRACTION100
1.38-1.410.18472710.13825129X-RAY DIFFRACTION100
1.41-1.440.1743010.12835159X-RAY DIFFRACTION100
1.44-1.470.1572740.1165183X-RAY DIFFRACTION100
1.47-1.510.14522820.10955153X-RAY DIFFRACTION100
1.51-1.550.14363040.1035161X-RAY DIFFRACTION100
1.55-1.590.14462890.10295152X-RAY DIFFRACTION100
1.59-1.640.14342840.10165189X-RAY DIFFRACTION100
1.64-1.70.13172650.10315204X-RAY DIFFRACTION100
1.7-1.770.13992770.10465202X-RAY DIFFRACTION100
1.77-1.850.14142710.10875223X-RAY DIFFRACTION100
1.85-1.950.14262550.11875212X-RAY DIFFRACTION100
1.95-2.070.13842500.11815244X-RAY DIFFRACTION100
2.07-2.230.15712810.12365281X-RAY DIFFRACTION100
2.23-2.460.15842950.12755221X-RAY DIFFRACTION100
2.46-2.810.16312810.14135311X-RAY DIFFRACTION100
2.81-3.540.17692820.15495342X-RAY DIFFRACTION100
3.54-52.380.16522930.16525565X-RAY DIFFRACTION100

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