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- PDB-1hdh: Arylsulfatase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1hdh
TitleArylsulfatase from Pseudomonas aeruginosa
ComponentsArylsulfatase
KeywordsHYDROLASE / SULFATASE / FORMYLGLYCINE HYDRATE
Function / homology
Function and homology information


arylsulfatase (type I) / arylsulfatase activity / phosphoric diester hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily ...Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.3 Å
AuthorsBoltes, I. / Czapinska, H. / Kahnert, A. / von Buelow, R. / Dirks, T. / Schmidt, B. / von Figura, K. / Kertesz, M.A. / Uson, I.
CitationJournal: Structure / Year: 2001
Title: 1.3 A Structure of Arylsulfatase from Pseudomonas Aeruginosa Establishes the Catalytic Mechanism of Sulfate Ester Cleavage in the Sulfatase Family.
Authors: Boltes, I. / Czapinska, H. / Kahnert, A. / von Buelow, R. / Dirks, T. / Schmidt, B. / von Figura, K. / Kertesz, M.A. / Uson, I.
History
DepositionNov 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_ref / struct_ref_seq
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _pdbx_struct_mod_residue.parent_comp_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.2May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arylsulfatase
B: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,88812
Polymers120,0392
Non-polymers84910
Water14,592810
1
A: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4446
Polymers60,0201
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4446
Polymers60,0201
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)188.920, 67.290, 89.700
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98902, -0.00177, -0.14774), (0.00126, -0.99999, 0.00354), (-0.14775, 0.00331, 0.98902)
Vector: 94.03252, 36.73586, 6.897)

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Components

#1: Protein Arylsulfatase / / AS / Aryl-sulfate sulphohydrolase


Mass: 60019.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: atsA, PA0183 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51691, arylsulfatase (type I)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PROTEIN SOLUTION: 11MG/ML IN 20 MM TRIS-HCL PH 7.5 + EQUAL VOLUME OF PRECIPITANT: 100 MM MES PH 6.3, 200 MM AMMONIUM SULFATE, 20% (W/V) PEG MONOMETHYLETHER 5000; HANGING DROP, 20 C
Crystal grow
*PLUS
Temperature: 18-22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
3100 mMMES1reservoirpH6.3
4200 mMammonium sulfate1reservoir
522 %(w/v)PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: BENT CRYSTAL
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 255817 / % possible obs: 93.1 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.7
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.5 / % possible all: 81.5
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 81.5 % / Rmerge(I) obs: 0.337

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
SHELXL-97refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.3→20 Å / Num. parameters: 36198 / Num. restraintsaints: 46182 / Cross valid method: FREE R-VALUE / σ(F): 0 / StereochEM target val spec case: CSD FOR DDZ 51 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 12843 5 %5%
all0.1996 255817 --
obs0.1987 -93.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 7763.36 / Occupancy sum non hydrogen: 8989.8
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8155 0 42 810 9007
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.033
X-RAY DIFFRACTIONs_from_restr_planes0.0294
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1894 / Rfactor Rfree: 0.2179 / Rfactor Rwork: 0.1885
Solvent computation
*PLUS
Displacement parameters
*PLUS

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