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- PDB-6f6j: Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

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Basic information

Entry
Database: PDB / ID: 6f6j
TitleCrystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine
ComponentsL-lysine 3-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Clavaminate synthase-like / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-CUW / : / SUCCINIC ACID / L-lysine 3-hydroxylase
Similarity search - Component
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIsabet, T. / Stura, E.A. / Legrand, P. / Zaparucha, A. / Bastard, K.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.
Authors: Bastard, K. / Isabet, T. / Stura, E.A. / Legrand, P. / Zaparucha, A.
History
DepositionDec 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Assembly

Deposited unit
A: L-lysine 3-hydroxylase
B: L-lysine 3-hydroxylase
C: L-lysine 3-hydroxylase
D: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,40718
Polymers156,9454
Non-polymers1,46314
Water22,8791270
1
A: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6315
Polymers39,2361
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5724
Polymers39,2361
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5724
Polymers39,2361
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6315
Polymers39,2361
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.950, 67.390, 110.650
Angle α, β, γ (deg.)107.55, 102.87, 93.58
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-lysine 3-hydroxylase / Alpha-ketoglutarate-dependent dioxygenase / KDO1 / L-lysine hydroxylase


Mass: 39236.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenulispora acidiphila (strain DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897) (bacteria)
Strain: DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_0231 / Production host: Escherichia coli (E. coli)
References: UniProt: C7QJ42, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 5 types, 1284 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-CUW / (2~{S},3~{R})-2,6-bis(azanyl)-3-oxidanyl-hexanoic acid / 3-hydroxy-L-lysine


Mass: 162.187 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14N2O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1270 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: KDO1: 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05 M Tris-HCl, pH 8 Precipitant: 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate. Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.2 M NaCl, 0. ...Details: KDO1: 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05 M Tris-HCl, pH 8 Precipitant: 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate. Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.2 M NaCl, 0.02 M Na Succinate, 0.001 M FeIISO4 (0.5 M stock solution prepared in 0.050 M dithionite), 0.05 M alpha-KG, 0.05 M L-Lysine, 20% glycerol
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 101680 / % possible obs: 99 % / Redundancy: 5.85 % / Biso Wilson estimate: 42.26 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0083 / Net I/σ(I): 13.63
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.985 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 7144 / CC1/2: 0.738 / Rrim(I) all: 0.833 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5025 4.94 %RANDOM
Rwork0.194 ---
obs0.196 101618 99.3 %-
Displacement parametersBiso mean: 52.52 Å2
Baniso -1Baniso -2Baniso -3
1--10.6515 Å20.7416 Å21.1629 Å2
2---1.7552 Å20.9926 Å2
3---12.4066 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10024 0 88 1270 11382
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110511HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0214287HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3619SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1611HARMONIC5
X-RAY DIFFRACTIONt_it10511HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion16.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13196SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 349 4.78 %
Rwork0.2178 6945 -
all0.2193 7294 -
obs--95.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76950.2036-0.17652.0617-0.35881.4920.0540.08050.1011-0.11790.03420.0730.0554-0.0019-0.0882-0.1541-0.00010.0250.0241-0.0355-0.0269-46.7093-60.4475-13.3869
20.52960.12090.11191.71440.30031.77120.098-0.1047-0.02730.4524-0.01710.23340.3373-0.2479-0.08090.1058-0.06730.04070.1128-0.0238-0.0261-56.5633-77.412813.7337
30.89260.2835-0.16562.3347-0.5371.66430.0704-0.1452-0.07080.2211-0.1172-0.033-0.13470.2030.0468-0.0996-0.0497-0.01140.0402-0.0323-0.0426-18.4046-93.0804-31.029
40.7573-0.2674-0.39161.6350.45111.5490.19120.16650.0238-0.5192-0.13330.1504-0.3459-0.1714-0.05790.16440.0398-0.00940.0918-0.0319-0.0616-27.5916-75.9734-58.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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