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

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Basic information

Entry
Database: PDB / ID: 2cfz
TitleCrystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, in complex with 1-dodecanol
ComponentsSDS HYDROLASE SDSA1
KeywordsHYDROLASE
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 / identical protein binding / metal ion 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; Chain A / Metallo-beta-lactamase superfamily / 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
1-DODECANOL / DI(HYDROXYETHYL)ETHER / Linear primary-alkylsulfatase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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.-D.
History
DepositionFeb 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary
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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SDS HYDROLASE SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3097
Polymers72,6731
Non-polymers6366
Water11,403633
1
A: SDS HYDROLASE SDSA1
hetero molecules

A: SDS HYDROLASE SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,61714
Polymers145,3462
Non-polymers1,27112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area13200 Å2
ΔGint-159.1 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.323, 86.323, 367.594
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 SDS HYDROLASE SDSA1 / SDSA21 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-1DO / 1-DODECANOL


Mass: 186.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 633 / 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, 0.2M CITRATE PH6, pH 6.00

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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 / Date: Mar 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 51984 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.9 / % possible all: 99.6

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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: 2.05→74.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.138 / SU ML: 0.104 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2651 5.1 %RANDOM
Rwork0.16 ---
obs0.163 49267 99.3 %-
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--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 36 633 5600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215406
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9657357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76123.099284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00715879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6691563
X-RAY DIFFRACTIONr_chiral_restr0.1010.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024331
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22596
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23671
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.523414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.25935293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.04222293
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.18632060
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: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 190
Rwork0.185 3522
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)
10.30680.11280.04120.23730.05680.31050.0234-0.0550.01160.0387-0.0217-0.0075-0.0038-0.0025-0.0016-0.09310.00510.0089-0.1137-0.0018-0.179437.95323.049173.386
20.28880.18320.06971.1488-0.13991.0220.00480.05930.10250.08050.05290.0164-0.3053-0.0163-0.05770.02820.05160.0226-0.07920.0016-0.098133.87650.578151.899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 523
2X-RAY DIFFRACTION2A531 - 654

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