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- PDB-4cxs: G4 mutant of PAS, arylsulfatase from Pseudomonas aeruginosa, in c... -

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Basic information

Entry
Database: PDB / ID: 4cxs
TitleG4 mutant of PAS, arylsulfatase from Pseudomonas aeruginosa, in complex with Phenylphosphonic acid
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
phenylphosphonic acid / Arylsulfatase / :
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiton, C.M. / Jonas, S. / Mohammed, M.F. / Fischer, G. / 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
DepositionApr 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
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: Atomic model / Data collection / Structure summary
Category: atom_site / pdbx_validate_chiral ...atom_site / pdbx_validate_chiral / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct
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 / _struct.title
Revision 3.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.2Dec 20, 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 / 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
Revision 3.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)121,01411
Polymers119,9512
Non-polymers1,0639
Water4,035224
1
A: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4285
Polymers59,9751
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5866
Polymers59,9751
Non-polymers6105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.528, 66.183, 89.338
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2085-

HOH

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Components

#1: Protein ARYLSULFATASE


Mass: 59975.484 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: U6AIT1, UniProt: P51691*PLUS, 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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SV7 / phenylphosphonic acid


Mass: 158.092 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H7O3P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: NONE
Crystal growpH: 6.3
Details: 0.1M MES PH=6.3, 32% W/V PEG5000 MME, 0.002 M (NH4)2SO4, 0.039 M PHENYLPHOSPHONIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8933
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8933 Å / Relative weight: 1
ReflectionResolution: 2.3→39.1 Å / Num. obs: 46978 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.7 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HDH

1hdh


Resolution: 2.3→91.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.249 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY 2 RESIDUES FROM N--TERMINUS AND 9 RESIDUES AT C-TERMINUS DISORDERED LOOP 75-84 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24379 2376 5.1 %RANDOM
Rwork0.20335 ---
obs0.20542 44589 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.06 Å2
2--0.92 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→91.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8196 0 62 224 8482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198480
X-RAY DIFFRACTIONr_bond_other_d0.0030.027867
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.96511532
X-RAY DIFFRACTIONr_angle_other_deg0.9693.00118039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6951032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30822.597412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.589151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9611584
X-RAY DIFFRACTIONr_chiral_restr0.1050.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219654
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022062
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_it1.7742.2724143
X-RAY DIFFRACTIONr_mcbond_other1.7742.2714142
X-RAY DIFFRACTIONr_mcangle_it2.9143.3945170
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0642.4864337
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: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 174 -
Rwork0.287 3214 -
obs--95.73 %

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