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

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Basic information

Entry
Database: PDB / ID: 1oij
TitleCrystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with alphaketoglutarate
Components(PUTATIVE ALKYLSULFATASE ...) x 3
KeywordsOXIDOREDUCTASE / JELLY ROLL
Function / homology
Function and homology information


alkyl sulfatase / dioxygenase activity / metal ion binding
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: 2.1 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)133,73312
Polymers133,0574
Non-polymers6768
Water12,448691
1
A: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4463
Polymers33,2761
Non-polymers1692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4173
Polymers33,2481
Non-polymers1692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4533
Polymers33,2831
Non-polymers1692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE ALKYLSULFATASE ATSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4173
Polymers33,2481
Non-polymers1692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.447, 144.876, 160.692
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, -0.001, -0.063), (0.001, -1), (-0.063, 0.998)1.03458, 1.48746, 0.01419
2given(0.999, 0.033, 0.042), (-0.05, 0.312, 0.949), (0.018, -0.949, 0.314)0.20811, 0.58879, 0.59361
3given(-0.999, -0.017, -0.027), (-0.02, -0.313, 0.949), (-0.025, 0.95, 0.313)1.31258, 1.04717, -0.6706

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Components

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PUTATIVE ALKYLSULFATASE ... , 3 types, 4 molecules ABDC

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


Mass: 33276.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5
#2: Protein PUTATIVE ALKYLSULFATASE ATSK / NON-HEME FE(II) ALPHA KETO GLUTARATE DEPENDENT DIOXYGENASE / ALKYLSULFATASE


Mass: 33248.402 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
#3: Protein PUTATIVE ALKYLSULFATASE ATSK / NON-HEME FE(II) ALPHA KETO GLUTARATE DEPENDENT DIOXYGENASE / ALKYLSULFATASE


Mass: 33283.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DSM 6884 / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5

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Non-polymers , 3 types, 699 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


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


Mass: 18.015 Da / Num. of mol.: 691 / 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: 3.17 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.5
Details: 50 MM NA ACETATE 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: 0.8126
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: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.07→38.92 Å / Num. obs: 102501 / % possible obs: 98.8 % / Redundancy: 4.65 % / Rmerge(I) obs: 0.1042 / Net I/σ(I): 13.51
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4099 / Mean I/σ(I) obs: 3.06 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 38.93 Å / Num. measured all: 472571 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 94.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.06

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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: 2.1→38.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.795 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4763 4.8 %RANDOM
Rwork0.191 ---
obs0.192 94338 100 %-
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: 35.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--2.51 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7708 0 44 691 8443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217934
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9310801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945969
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_restr0.1160.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23253
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2525
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.46124879
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.82247848
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.74543055
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.98962953
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: 1817 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.070.05
3Ctight positional0.070.05
4Dtight positional0.070.05
1Atight thermal0.230.5
2Btight thermal0.230.5
3Ctight thermal0.230.5
4Dtight thermal0.250.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 40
Rwork0.238 7208
Refinement
*PLUS
Lowest resolution: 38.93 Å / % reflection Rfree: 4.8 %
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_deg1.6

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