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- PDB-6f2b: Crystal structure of the complex Fe(II)/alpha-ketoglutarate depen... -

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Basic information

Entry
Database: PDB / ID: 6f2b
TitleCrystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/alpha-ketoglutarate
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 / 2-OXOGLUTARIC ACID / : / L-lysine 3-hydroxylase
Function and homology information
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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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)157,75312
Polymers156,9454
Non-polymers8088
Water20,9511163
1
A: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4383
Polymers39,2361
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4383
Polymers39,2361
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4383
Polymers39,2361
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: L-lysine 3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4383
Polymers39,2361
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.820, 67.970, 110.430
Angle α, β, γ (deg.)107.78, 102.79, 93.45
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
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 alpha-ketoglutarate, 20% glycerol, 10 minute soaking
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: Mar 26, 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. obs: 101974 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.04 Å2 / Rrim(I) all: 0.01 / Net I/σ(I): 10.86
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Num. unique obs: 7151 / Rrim(I) all: 0.1125 / % possible all: 93.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Cootmodel building
XDSdata reduction
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBQ

2wbq


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.201 5024 4.94 %RANDOM
Rwork0.171 ---
obs0.173 101786 99.1 %-
Displacement parametersBiso mean: 45.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.237 Å21.8992 Å2-1.1863 Å2
2---5.9231 Å23.8793 Å2
3---7.1601 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9863 0 44 1163 11070
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110344HARMONIC2
X-RAY DIFFRACTIONt_angle_deg114079HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1587HARMONIC5
X-RAY DIFFRACTIONt_it10344HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion16.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1357SEMIHARMONIC5
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_contact12784SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2452 350 4.77 %
Rwork0.2309 6981 -
all0.2317 7331 -
obs--96.6 %
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)
10.9609-0.0086-0.07231.1527-0.1511.14970.02780.0360.0812-0.0530.03520.02130.001-0.0366-0.0630.0050.0131-0.00010.0460.00440.0568-46.6695-60.94-13.6511
20.65060.14320.14911.13750.64061.63680.085-0.127-0.03770.2745-0.07770.12250.3402-0.2695-0.00740.2401-0.0602-0.00420.24290.02630.1115-56.5652-77.899713.4889
31.17030.2751-0.08121.4584-0.34411.08560.0387-0.0909-0.08030.0964-0.04130.0033-0.0560.08950.00270.0557-0.0186-0.00370.08810.00530.0829-18.3166-93.88-30.6565
40.6749-0.1299-0.2720.95280.64481.53940.10810.16770.063-0.3127-0.11210.1022-0.3372-0.2020.0040.24640.0469-0.01180.20170.01410.0932-28.2262-76.7394-58.2216
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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