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- PDB-5aj9: G7 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5aj9
TitleG7 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa
ComponentsARYLSULFATASE
KeywordsHYDROLASE / CATALYTIC PROMISCUITY / DIRECTED EVOLUTION / NEUTRAL DRIFT / SULFATASE / SUPERFAMILY
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiton, C.M. / Fischer, G. / Jonas, S. / Mohammed, M.F. / Loo, B.v. / Kintses, B. / Hyvonen, M. / Tokuriki, N. / Hollfelder, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset.
Authors: Miton, C.M. / Jonas, S. / Fischer, G. / Duarte, F. / Mohamed, M.F. / van Loo, B. / Kintses, B. / Kamerlin, S.C.L. / Tokuriki, N. / Hyvonen, M. / Hollfelder, F.
History
DepositionFeb 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jan 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 3.0Apr 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 3.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / software / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: ARYLSULFATASE
B: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,79329
Polymers119,7192
Non-polymers2,07427
Water7,566420
1
A: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87313
Polymers59,8591
Non-polymers1,01412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,91916
Polymers59,8591
Non-polymers1,06015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.399, 66.496, 89.435
Angle α, β, γ (deg.)90.00, 93.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2158-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ARYLSULFATASE


Mass: 59859.273 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PRSF-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: U5R2L4, UniProt: P51691*PLUS, arylsulfatase (type I)

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Non-polymers , 5 types, 447 molecules

#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


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growDetails: 32% PEG 5000 MME, 0.2M (NH4)2SO4, 0.1M MES PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→29.3 Å / Num. obs: 67936 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 50.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→91.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY, BUT HAVE NOT BEEN WRITTEN INTO THE PDB FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.24779 3461 5.1 %RANDOM
Rwork0.20065 ---
obs0.20302 64415 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.483 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20.43 Å2
2--0.71 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2→91.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8308 0 101 420 8829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198504
X-RAY DIFFRACTIONr_bond_other_d0.0010.027857
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.96511588
X-RAY DIFFRACTIONr_angle_other_deg3.724318007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69551054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42122.711391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.483151263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0211574
X-RAY DIFFRACTIONr_chiral_restr0.0990.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219651
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022019
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5343.0094216
X-RAY DIFFRACTIONr_mcbond_other2.5323.0094215
X-RAY DIFFRACTIONr_mcangle_it3.6614.5085270
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2163.3414288
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 254 -
Rwork0.328 4459 -
obs--87.7 %

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