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- PDB-6eur: Crystal structure of the complex Fe(II)/alpha-ketoglutarate depen... -

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Basic information

Entry
Database: PDB / ID: 6eur
TitleCrystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/alpha-ketoglutarate
ComponentsL-lysine 4-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase
Function / homologyOxidoreductases; 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 / Taurine dioxygenase TauD-like superfamily / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / 2-OXOGLUTARIC ACID / : / L-lysine 4-hydroxylase
Function and homology information
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIsabet, T. / Stura, E. / 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
DepositionOct 31, 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: L-lysine 4-hydroxylase
B: L-lysine 4-hydroxylase
C: L-lysine 4-hydroxylase
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,99722
Polymers167,2694
Non-polymers1,72918
Water12,304683
1
A: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3877
Polymers41,8171
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1114
Polymers41,8171
Non-polymers2943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2956
Polymers41,8171
Non-polymers4785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2035
Polymers41,8171
Non-polymers3864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.420, 99.460, 166.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-lysine 4-hydroxylase / Alpha-ketoglutarate-dependent dioxygenase / KDO5 / L-lysine hydroxylase


Mass: 41817.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. (strain CF136) (bacteria)
Strain: CF136 / Gene: PMI10_03368 / Production host: Escherichia coli (E. coli)
References: UniProt: J3BZS6, 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: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Imidazole malate pH 7.0 25% w/v PEG 4000 0.15M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.3→33.7 Å / Num. obs: 59249 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.56 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 0.159
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.12 / Rrim(I) all: 1.48 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Cootmodel building
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.405 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.451 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2846 4.8 %RANDOM
Rwork0.174 ---
obs0.176 59249 87.1 %-
Displacement parametersBiso mean: 59.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.9918 Å20 Å20 Å2
2--1.5178 Å20 Å2
3----5.5097 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 104 683 11558
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111251HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1415227HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3910SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes307HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1632HARMONIC5
X-RAY DIFFRACTIONt_it11251HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1449SEMIHARMONIC5
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_contact13257SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2471 -5.04 %
Rwork0.2171 1847 -
all0.2186 1945 -
obs--39.16 %
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)
11.4746-0.1904-0.23481.84020.3121.850.0141-0.13680.03530.33120.1758-0.20680.21550.175-0.1899-0.01980.0216-0.1166-0.0535-0.0418-0.13680.154261.320633.9166
21.70870.4456-0.2472.18880.38162.53540.00250.17920.1942-0.48160.1646-0.1055-0.5638-0.0849-0.16710.31290.01470.05220.17390.05090.1428-0.838177.98422.2431
31.55840.0168-0.08681.46570.55612.66980.0882-0.0552-0.14740.39890.0583-0.03330.94530.0464-0.14650.54650.0014-0.04870.15850.00380.0557-0.38923.0885-1.7883
42.7280.81110.87592.64961.53233.0836-0.01330.66440.0859-0.50280.3774-0.2645-0.30180.7653-0.3640.1774-0.03630.14170.3699-0.01030.00334.242138.8661-33.6599
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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