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- PDB-6w1k: Crystal structure of the hydroxyglutarate synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6w1k
TitleCrystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Oryza sativa
ComponentsHydroxyglutarate synthase
KeywordsLYASE / Decarboxylase Lysine catabolism
Function / homology
Function and homology information


2-oxoadipate dioxygenase/decarboxylase / amyloplast / dioxygenase activity / chloroplast / metal ion binding
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 - #50 / 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, chloroplastic/amyloplastic / 2-oxoadipate dioxygenase/decarboxylase, chloroplastic/amyloplastic
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyglutarate synthase
B: Hydroxyglutarate synthase
C: Hydroxyglutarate synthase
D: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,97328
Polymers144,5614
Non-polymers2,41224
Water20,2311123
1
A: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5515
Polymers36,1401
Non-polymers4114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8398
Polymers36,1401
Non-polymers6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8398
Polymers36,1401
Non-polymers6997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hydroxyglutarate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7437
Polymers36,1401
Non-polymers6036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.300, 98.200, 203.800
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: 36140.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OsJ_31810, OSJNBa0071K18.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H916, UniProt: Q337M4*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1123 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01 M Magnesium Chloride, 0.05 M MES pH 5.6, 1.8 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→39.8 Å / Num. obs: 156493 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.91 Å / Num. unique obs: 15364 / CC1/2: 0.517

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LHO

3lho


Resolution: 1.85→39.79 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4898
RfactorNum. reflection% reflection
Rfree0.1915 7752 4.95 %
Rwork0.1646 --
obs0.1659 156470 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9784 0 128 1123 11035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110149
X-RAY DIFFRACTIONf_angle_d1.086113764
X-RAY DIFFRACTIONf_chiral_restr0.05881475
X-RAY DIFFRACTIONf_plane_restr0.00771795
X-RAY DIFFRACTIONf_dihedral_angle_d18.18663701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.31892510.29994840X-RAY DIFFRACTION98.74
1.87-1.890.30972460.27014921X-RAY DIFFRACTION98.89
1.89-1.920.29242800.24944826X-RAY DIFFRACTION98.42
1.92-1.940.28072710.24144897X-RAY DIFFRACTION98.68
1.94-1.970.25992400.23434931X-RAY DIFFRACTION98.72
1.97-1.990.26922560.22694866X-RAY DIFFRACTION98.82
1.99-2.020.26142460.22964954X-RAY DIFFRACTION98.86
2.02-2.050.24912500.20964937X-RAY DIFFRACTION98.99
2.05-2.080.23382520.19724895X-RAY DIFFRACTION99
2.08-2.120.23262640.18694889X-RAY DIFFRACTION99.25
2.12-2.150.21682790.18114936X-RAY DIFFRACTION99.13
2.15-2.190.21022690.17064800X-RAY DIFFRACTION96.63
2.19-2.240.21322720.15974933X-RAY DIFFRACTION99.41
2.24-2.280.20932580.15244967X-RAY DIFFRACTION99.43
2.28-2.330.18622760.15424916X-RAY DIFFRACTION99.33
2.33-2.380.1952630.15734940X-RAY DIFFRACTION99.35
2.39-2.440.18482590.15154951X-RAY DIFFRACTION99.26
2.44-2.510.20072560.15244955X-RAY DIFFRACTION99.33
2.51-2.580.18892520.15455019X-RAY DIFFRACTION99.55
2.58-2.670.16822390.15334973X-RAY DIFFRACTION99.69
2.67-2.760.19232510.15634992X-RAY DIFFRACTION99.51
2.76-2.870.1942760.15844840X-RAY DIFFRACTION96.93
2.87-30.21272570.16195024X-RAY DIFFRACTION99.68
3-3.160.19522540.16945025X-RAY DIFFRACTION99.68
3.16-3.360.18812630.16514998X-RAY DIFFRACTION99.66
3.36-3.620.17282390.15745063X-RAY DIFFRACTION99.55
3.62-3.980.16632460.14275075X-RAY DIFFRACTION99.4
3.98-4.560.13552270.12144980X-RAY DIFFRACTION97.29
4.56-5.740.17252840.14095144X-RAY DIFFRACTION99.87
5.74-39.790.17992760.19335231X-RAY DIFFRACTION97.75

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