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- PDB-6f9p: Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

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Basic information

Entry
Database: PDB / ID: 6f9p
TitleCrystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Re(II)
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 / RHENIUM / L-lysine 4-hydroxylase
Function and homology information
Biological speciesFlavobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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
DepositionDec 15, 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

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)168,53516
Polymers167,2694
Non-polymers1,26712
Water3,045169
1
A: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2315
Polymers41,8171
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0393
Polymers41,8171
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0393
Polymers41,8171
Non-polymers2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2275
Polymers41,8171
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.200, 98.870, 165.960
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)
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

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Non-polymers , 5 types, 181 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-RE / RHENIUM


Mass: 186.207 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Re
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
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: 1.1761 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1761 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 58758 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 67.98 Å2 / Rrim(I) all: 0.125 / Net I/σ(I): 15.15
Reflection shellResolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.2 / Rrim(I) all: 1.662 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PARROTphasing
XSCALEdata scaling
BUCCANEERmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.367 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2925 4.98 %RANDOM
Rwork0.194 ---
obs0.195 58757 100 %-
Displacement parametersBiso mean: 83.81 Å2
Baniso -1Baniso -2Baniso -3
1--13.265 Å20 Å20 Å2
2---5.5538 Å20 Å2
3---18.8188 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.4→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 29 169 10605
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1114472HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes290HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1541HARMONIC5
X-RAY DIFFRACTIONt_it10698HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion17.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1380SEMIHARMONIC5
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_contact12150SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2764 212 4.95 %
Rwork0.2479 4071 -
all0.2493 4283 -
obs--99.88 %
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)
11.1143-0.4381-0.26811.68070.1661.80370.0174-0.1390.02780.17950.0629-0.07120.16550.1292-0.08030.019-0.0425-0.0562-0.1608-0.0002-0.2074-0.049861.004633.8617
21.4490.348-0.15681.86650.85492.21820.02340.12960.1331-0.58780.0526-0.0356-0.7722-0.0966-0.07610.33610.02750.0511-0.24270.07-0.2317-0.674577.76852.3347
31.6137-0.1258-0.02161.90730.65022.98040.105-0.041-0.2190.63320.03870.07521.1578-0.0435-0.14370.67-0.0217-0.0503-0.14570.0154-0.1328-0.118523.1077-1.7944
42.5820.70630.75551.95260.73222.65090.00690.74450.0253-0.27250.2079-0.1007-0.09960.5158-0.21480.0490.01740.06010.20940.0039-0.16864.399738.8912-33.4636
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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