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

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Basic information

Entry
Database: PDB / ID: 6euo
TitleCrystal structure of APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5
ComponentsL-lysine 4-hydroxylase
KeywordsOXIDOREDUCTASE / "Fe(II)/alpha-ketoglutarate
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 / : / D-MALATE / 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 30, 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)168,96122
Polymers167,2694
Non-polymers1,69318
Water9,458525
1
A: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2876
Polymers41,8171
Non-polymers4705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1915
Polymers41,8171
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3797
Polymers41,8171
Non-polymers5626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1034
Polymers41,8171
Non-polymers2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.280, 98.930, 166.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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)
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

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Non-polymers , 5 types, 543 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% PEG 3350, 200mM Imidazole malate pH7, 150mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→62.2 Å / Num. obs: 67467 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 56.78 Å2 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5 % / Num. unique obs: 4925 / CC1/2: 0.547 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3354 4.97 %RANDOM
Rwork0.169 ---
obs0.171 67467 100 %-
Displacement parametersBiso mean: 70.91 Å2
Baniso -1Baniso -2Baniso -3
1--5.0342 Å20 Å20 Å2
2---11.0676 Å20 Å2
3---16.1018 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→62.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10905 0 97 525 11527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.115475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3972SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes317HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1659HARMONIC5
X-RAY DIFFRACTIONt_it11419HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion18.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1473SEMIHARMONIC5
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_contact13596SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2858 246 4.99 %
Rwork0.236 4679 -
all0.2385 4925 -
obs--99.98 %
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)
11.1993-0.2221-0.3071.60970.40391.7602-0.0196-0.14270.02220.20530.1322-0.0890.14070.1631-0.1125-0.2378-0.0099-0.0606-0.2046-0.0204-0.2625-0.167960.915333.8265
21.61440.5556-0.31871.79870.42331.994-0.03320.15070.1472-0.54080.1217-0.0184-0.6603-0.0382-0.08850.6848-0.00970.03870.4060.05150.4169-0.774777.78252.2466
31.51130.06770.24351.23510.61693.03690.18250.0028-0.20870.4554-0.00020.01021.18880.0801-0.18230.88350.0218-0.05880.3404-0.010.3722-0.317322.8972-1.8942
42.62030.72780.82751.72270.9682.94890.0020.82910.0801-0.21660.2969-0.0706-0.12640.785-0.2990.25160.01920.08710.60450.00070.23534.597838.8624-33.6167
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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