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- PDB-1oii: Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) a... -

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Basic information

Entry
Database: PDB / ID: 1oii
TitleCrystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with iron and alphaketoglutarate
ComponentsPUTATIVE ALKYLSULFATASE ATSK
KeywordsOXIDOREDUCTASE / JELLY ROLL
Function / homology
Function and homology information


alkyl sulfatase / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMueller, I. / Kahnert, A. / Pape, T. / Dierks, T. / Meyer-Klauke, W. / Kertesz, M.A. / Uson, I.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of the Alkylsulfatase Atsk: Insights Into the Catalytic Mechanism of the Fe(II) Alpha-Ketoglutarate-Dependent Dioxygenase Superfamily
Authors: Mueller, I. / Kahnert, A. / Pape, T. / Sheldrick, G.M. / Meyer-Klaucke, W. / Dierks, T. / Kertesz, M.A. / Uson, I.
History
DepositionJun 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ALKYLSULFATASE ATSK
B: PUTATIVE ALKYLSULFATASE ATSK
C: PUTATIVE ALKYLSULFATASE ATSK
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,80112
Polymers132,9944
Non-polymers8088
Water10,323573
1
A: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4503
Polymers33,2481
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4503
Polymers33,2481
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4503
Polymers33,2481
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4503
Polymers33,2481
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.421, 147.329, 158.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A13 - 80
2111B13 - 80
3111C13 - 80
4111D13 - 80
1211A103 - 165
2211B103 - 165
3211C103 - 165
4211D103 - 165
1311A191 - 299
2311B191 - 299
3311C191 - 299
4311D191 - 299

NCS oper:
IDCodeMatrixVector
1given(-0.998, -0.008, -0.063), (0.008, -1, -0.001), (-0.063, -0.002, 0.998)1.05038, 1.48264, 0.01633
2given(0.999, -0.038, 0.013), (0.022, 0.234, -0.972), (0.034, 0.972, 0.234)-0.1883, 0.51786, -0.71707
3given(-0.999, -0.026, -0.034), (-0.027, -0.227, 0.973), (-0.033, 0.973, 0.226)1.32985, 0.96305, -0.69451

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Components

#1: Protein
PUTATIVE ALKYLSULFATASE ATSK / NON-HEME FE(II) ALPHA KETO GLUTARATE DEPENDENT DIOXYGENASE / ALKYLSULFATASE


Mass: 33248.402 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5
#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.: 573 / 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: 3.18 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.6
Details: 50 MM NA SULFATE, 50 MM NA CITRATE PH 5.5, 10% PEG 4000, 30% GLYCEROL
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlenzyme1drop
220 mMTris-HCl1droppH7.5
325 mMammonium acetate1reservoiror 25-50mM ammonium sulfate
425 mMsodium citrate1reservoirpH5.6
56-7 %PEG40001reservoir
630 %glycerol1reservoiror MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8098
DetectorType: MARRESEARCH / Detector: CCD / Details: PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8098 Å / Relative weight: 1
ReflectionResolution: 2.19→20 Å / Num. obs: 86268 / % possible obs: 97.5 % / Redundancy: 6.38 % / Rmerge(I) obs: 0.0644 / Net I/σ(I): 19.96
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 5.61 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 5.1 / % possible all: 83.1
Reflection
*PLUS
Highest resolution: 2.19 Å / Lowest resolution: 20 Å / Num. measured all: 564785 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 83.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OIH

1oih


Resolution: 2.19→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.18 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4246 4.9 %RANDOM
Rwork0.195 ---
obs0.197 81913 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2--1.71 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7594 0 44 573 8211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0217803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.92810647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026036
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.23238
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2539
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5424900
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.86347836
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.68842903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.58962811
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1755 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.060.05
3Ctight positional0.060.05
4Dtight positional0.060.05
1Atight thermal0.240.5
2Btight thermal0.250.5
3Ctight thermal0.230.5
4Dtight thermal0.290.5
LS refinement shellResolution: 2.19→2.24 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.345 117
Rwork0.256 4242
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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