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- PDB-6f2a: Crystal structure of the complex Fe(II)/alpha-ketoglutarate depen... -

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Basic information

Entry
Database: PDB / ID: 6f2a
TitleCrystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/Lysine
ComponentsL-lysine 3-hydroxylase
KeywordsOXIDOREDUCTASE / Fe(II)/alpha-ketoglutarate / dioxygenases / enzyme / FeII alphaKG form / oxydoreductase
Function / homology
Function and homology information


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-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Clavaminate synthase-like / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
ACETIC ACID / : / LYSINE / L-lysine 3-hydroxylase
Similarity search - Component
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / 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 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)158,24019
Polymers156,9454
Non-polymers1,29515
Water12,719706
1
A: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7427
Polymers39,2361
Non-polymers5066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4393
Polymers39,2361
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5595
Polymers39,2361
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4994
Polymers39,2361
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.940, 67.020, 110.750
Angle α, β, γ (deg.)107.48, 102.76, 93.74
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 721 molecules

#2: Chemical
ChemComp-FE2 / FE (II) 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
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, 0.05 M 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, 0.2 M NaCl, 0. ...Details: KDO1: 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05 M 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, 0.2 M NaCl, 0.02 M Na Succinate, 0.001 M FeIISO4 (0.5 M stock solution prepared in 0.050 M dithionite), 0.05 M L-Lysine, 20% glycerol
PH range: 7.5-8.0 / Temp details: air conditioned room

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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: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 402715 / Num. obs: 100281 / % possible obs: 97.9 % / Redundancy: 4.02 % / Biso Wilson estimate: 41.95 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.0118 / Net I/σ(I): 8.29
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.96 % / Mean I/σ(I) obs: 1.19 / CC1/2: 0.572 / Rrim(I) all: 0.124 / % possible all: 92

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Cootmodel building
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20.16 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4956 4.95 %RANDOM
Rwork0.203 ---
obs0.204 100086 98.3 %-
Displacement parametersBiso mean: 51.29 Å2
Baniso -1Baniso -2Baniso -3
1--12.1302 Å20.5826 Å2-0.4189 Å2
2--0.8446 Å22.5535 Å2
3---11.2855 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10023 0 25 706 10754
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110400HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0414124HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3561SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes222HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1573HARMONIC5
X-RAY DIFFRACTIONt_it10355HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion15.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1379SEMIHARMONIC5
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_contact12404SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 343 4.73 %
Rwork0.223 6908 -
all0.224 7251 -
obs--95.75 %
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)
10.71040.2862-0.14512.4548-0.34561.50350.03550.07290.0835-0.11740.07930.07940.0627-0.001-0.1148-0.0515-0.01320.05870.0366-0.01290.0591-46.5203-60.9983-13.0984
20.5570.30160.13042.26630.12631.60240.1328-0.0868-0.00050.58710.00450.29390.2618-0.2078-0.13730.279-0.06150.08590.14090.0050.1027-56.1679-77.713214.4085
30.8730.2846-0.19132.3359-0.63181.82940.0827-0.1219-0.03770.2095-0.1345-0.0553-0.18240.22710.05190.0325-0.06480.01010.0924-0.00860.0592-18.3186-93.2362-30.5721
40.6612-0.2004-0.51021.81040.34621.85790.21870.11470.0324-0.5034-0.13240.1254-0.3818-0.1413-0.08630.29560.02830.02780.1149-0.00870.0709-27.1934-76.2347-58.1515
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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