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- PDB-6f2e: Crystal structure of the APO Fe(II)/alpha-ketoglutarate dependent... -

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Basic information

Entry
Database: PDB / ID: 6f2e
TitleCrystal structure of the APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1
ComponentsL-lysine 3-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase
Function / homologyClavaminate synthase-like / 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 / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / ACETIC ACID / L-lysine 3-hydroxylase
Function and homology information
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionNov 24, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)157,1858
Polymers156,9454
Non-polymers2404
Water24,1941343
1
A: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2962
Polymers39,2361
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2962
Polymers39,2361
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2962
Polymers39,2361
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2962
Polymers39,2361
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.650, 68.090, 110.220
Angle α, β, γ (deg.)107.85, 102.84, 93.23
Int Tables number1
Space group name H-MP1

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Components

#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)
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
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1343 / 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: 50.63 %
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, 0.05M 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, 0.3 M Na Acetate, 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: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 117676 / % possible obs: 98.5 % / Redundancy: 4.65 % / Biso Wilson estimate: 29.66 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.0117 / Net I/σ(I): 10.24
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 29174 / CC1/2: 0.668 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5883 5 %RANDOM
Rwork0.177 ---
obs0.178 117663 98.6 %-
Displacement parametersBiso mean: 37.56 Å2
Baniso -1Baniso -2Baniso -3
1--2.862 Å20.4597 Å2-0.1197 Å2
2---4.8629 Å22.7835 Å2
3---7.725 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10076 0 16 1343 11435
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110603HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9714437HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3661SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1630HARMONIC5
X-RAY DIFFRACTIONt_it10603HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion15.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1393SEMIHARMONIC5
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_contact13653SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2474 422 5 %
Rwork0.2291 8021 -
all0.23 8443 -
obs--95.63 %
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)
10.7727-0.11160.00860.9112-0.131.01460.03020.01250.073-0.03660.01280.0006-0.0275-0.0002-0.043-0.0042-0.0023-0.0020.04910.010.0326-46.608-60.9983-13.5157
20.63210.09030.04021.02090.6451.52670.0699-0.0906-0.0320.2357-0.08610.10390.3283-0.28790.01620.2369-0.077-0.00570.28340.02670.1153-56.3893-78.218113.3774
31.0080.2557-0.09771.0939-0.21790.68650.0282-0.0674-0.08810.0494-0.03610.0071-0.01810.06530.00780.0309-0.018-0.00990.08220.01410.0526-18.5689-94.4228-31.3855
40.6574-0.1254-0.17340.95280.61971.37510.0940.14330.0409-0.2662-0.12010.0947-0.3144-0.21060.02610.24670.0538-0.01590.23330.0240.1008-27.6534-77.0555-58.2216
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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