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

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Basic information

Entry
Database: PDB / ID: 6exf
TitleCrystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/Lysine
ComponentsL-lysine 4-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII Lysine form
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 / : / LYSINE / L-lysine 4-hydroxylase
Function and homology information
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionNov 8, 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)168,41215
Polymers167,2694
Non-polymers1,14411
Water14,502805
1
A: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1674
Polymers41,8171
Non-polymers3503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0203
Polymers41,8171
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1124
Polymers41,8171
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1124
Polymers41,8171
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.721, 99.618, 165.819
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. (bacteria) / 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-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 4000, 0.2M Imidazole Malate pH 7.0, 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: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 110794 / % possible obs: 99.5 % / Redundancy: 7.07 % / Biso Wilson estimate: 49.44 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 13.93
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 5.64 % / Mean I/σ(I) obs: 0.28 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.186 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3788 4.96 %RANDOM
Rwork0.177 ---
obs0.179 76433 68.8 %-
Displacement parametersBiso mean: 60.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.7402 Å20 Å20 Å2
2--0.6056 Å20 Å2
3----2.3458 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10805 0 16 805 11626
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111234HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0715219HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3918SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes313HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1627HARMONIC5
X-RAY DIFFRACTIONt_it11234HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion17.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1446SEMIHARMONIC5
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_contact13349SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2832 -1.37 %
Rwork0.2683 289 -
all0.2685 293 -
obs--3.64 %
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)
11.1468-0.2648-0.19821.46660.24521.7530.0368-0.1473-0.00930.26460.1211-0.15010.21070.1655-0.1580.15870.0054-0.11810.1303-0.01290.1039-0.183561.170833.968
21.48570.371-0.31641.73680.18852.14190.0080.14480.1399-0.36160.1253-0.0634-0.526-0.1101-0.13320.34280.02530.02710.190.03680.2044-0.783278.20082.31
31.41790.0342-0.12491.47420.38561.84240.1008-0.1087-0.1250.38070.0452-0.07690.72180.0169-0.1460.5321-0.0021-0.05470.22450.0050.1569-0.133722.9828-1.5167
42.35650.73310.79422.37081.41262.6674-0.04810.56280.0612-0.43420.3641-0.2799-0.26550.6546-0.3160.2207-0.05180.14110.3812-0.01990.12434.277739.0492-33.6349
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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