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- PDB-2cg2: Crystal structure of SdsA1, an alkylsulfatase from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 2cg2
TitleCrystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, in complex with sulfate
ComponentsSDSA1
KeywordsHYDROLASE / SDS-HYDROLASE / SDSA1 / PSEUDOMONAS AERUGINOSA
Function / homology
Function and homology information


linear primary-alkylsulfatase / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / outer membrane-bounded periplasmic space / protein dimerization activity / metal ion binding / identical protein binding
Similarity search - Function
Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / : / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain ...Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / : / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Linear primary-alkylsulfatase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHagelueken, G. / Adams, T.M. / Wiehlmann, L. / Widow, U. / Kolmar, H. / Tuemmler, B. / Heinz, D.W. / Schubert, W.-D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: The Crystal Structure of Sdsa1, an Alkylsulfatase from Pseudomonas Aeruginosa, Defines a Third Class of Sulfatases.
Authors: Hagelueken, G. / Adams, T.M. / Wiehlmann, L. / Widow, U. / Kolmar, H. / Tummler, B. / Heinz, D.W. / Schubert, W.
History
DepositionFeb 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9004
Polymers72,6731
Non-polymers2273
Water7,584421
1
A: SDSA1
hetero molecules

A: SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8008
Polymers145,3462
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
MethodPQS
Unit cell
Length a, b, c (Å)85.662, 85.662, 364.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SDSA1 / PROBABLE BETA-LACTAMASE


Mass: 72673.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I5I9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 6
Details: 12% PEG4000, 10% ISOPROPANOL, 0.2M LICL, 0.1M CITRATE PH6, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8048
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8048 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 46750 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG3

2cg3


Resolution: 2.1→74.12 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.916 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2375 5.1 %RANDOM
Rwork0.166 ---
obs0.168 44374 98.9 %-
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: 24.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 7 421 5351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9617376
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31223.171287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69515890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8341564
X-RAY DIFFRACTIONr_chiral_restr0.0970.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024370
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22803
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23721
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2533
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2157
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.53426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29725335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.22232261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3974.52036
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
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.221 189
Rwork0.179 3173

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