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

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Basic information

Entry
Database: PDB / ID: 1oik
TitleCrystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with fe, alphaketoglutarate and 2-ethyl-1-hexanesulfuric acid
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 / (2R)-2-ETHYL-1-HEXANESULFONIC ACID / : / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3778
Polymers66,5532
Non-polymers8246
Water4,414245
1
A: PUTATIVE ALKYLSULFATASE ATSK
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules

A: PUTATIVE ALKYLSULFATASE ATSK
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,75516
Polymers133,1064
Non-polymers1,64912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x,-y+1,-z+1/21
Buried area10400 Å2
ΔGint-57.93 kcal/mol
Surface area37130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.027, 141.892, 161.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A13 - 80
2111D13 - 80
1212A103 - 165
2212D103 - 165
1313A191 - 299
2313D191 - 299

NCS oper: (Code: given
Matrix: (-1, 0.016, 0.016), (0.009, -0.373, 0.928), (0.021, 0.928, 0.372)
Vector: 1.24234, 0.41967, -0.25731)

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Components

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


Mass: 33276.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5
#2: Chemical ChemComp-C26 / (2R)-2-ETHYL-1-HEXANESULFONIC ACID


Mass: 210.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4S
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.5 / Details: pH 5.50
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: 0.8111
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: 0.8111 Å / Relative weight: 1
ReflectionResolution: 2.06→25 Å / Num. obs: 51154 / % possible obs: 99.1 % / Observed criterion σ(I): 13.53 / Redundancy: 5.24 % / Rmerge(I) obs: 0.0571 / Net I/σ(I): 4.34
Reflection shellResolution: 2.06→2.15 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.3209 / Mean I/σ(I) obs: 4.34 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 25 Å / Num. measured all: 270566 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.34

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Processing

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

1oih


Resolution: 2.06→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.97 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2581 5 %RANDOM
Rwork0.199 ---
obs0.2 48534 99.9 %-
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: 49.21 Å2
Baniso -1Baniso -2Baniso -3
1--3.72 Å20 Å20 Å2
2--3.76 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.06→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 48 245 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9285389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245487
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_restr0.1270.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21647
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.77222452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.16243926
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.92741502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.84661463
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1841 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.070.05
tight thermal0.340.5
LS refinement shellResolution: 2.06→2.11 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 199
Rwork0.271 3355
Refinement
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 %
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_deg1.68

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