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- PDB-4cyr: G4 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4cyr
TitleG4 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
DI(HYDROXYETHYL)ETHER / Arylsulfatase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 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 2.0Apr 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 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Oct 23, 2024Group: Data collection / Database references ...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 / 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)121,31017
Polymers119,9512
Non-polymers1,35915
Water21,8881215
1
A: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,91011
Polymers59,9751
Non-polymers93510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4006
Polymers59,9751
Non-polymers4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)188.496, 67.682, 89.518
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2408-

HOH

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Components

#1: Protein ARYLSULFATASE / AS / ARYL-SULFATE SULPHOHYDROLASE


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: P51691, arylsulfatase (type I)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1215 / 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: 48.29 % / Description: NONE
Crystal growpH: 6.3
Details: 0.1 M MES PH 6.3, 27 % (W/V) PEG 5000 MME, 0.16 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.011
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 2, 2012 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.011 Å / Relative weight: 1
ReflectionResolution: 1.72→67.09 Å / Num. obs: 119433 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.72→1.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→94.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.836 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES - REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20306 4075 3.4 %RANDOM
Rwork0.17602 ---
obs0.17717 115357 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.18 Å2
2--1.71 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.72→94.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8311 0 73 1215 9599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198643
X-RAY DIFFRACTIONr_bond_other_d0.0050.028016
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.96611759
X-RAY DIFFRACTIONr_angle_other_deg1.151318401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69351058
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13922.601419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.771151333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1181586
X-RAY DIFFRACTIONr_chiral_restr0.1430.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219838
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022072
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_it1.7481.7034226
X-RAY DIFFRACTIONr_mcbond_other1.7471.7024225
X-RAY DIFFRACTIONr_mcangle_it2.632.5495286
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.722.0264417
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: 1.716→1.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 326 -
Rwork0.268 8434 -
obs--98.95 %

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