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- PDB-4cxu: G4 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa, in c... -

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Basic information

Entry
Database: PDB / ID: 4cxu
TitleG4 mutant of PAS, arylsulfatase from Pseudomonas Aeruginosa, in complex with 3-Br-Phenolphenylphosphonate
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
3-bromophenyl hydrogen (S)-phenylphosphonate / Arylsulfatase / :
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 1.0Apr 22, 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 2.2Dec 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.3Oct 16, 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)120,6576
Polymers119,9512
Non-polymers7064
Water11,980665
1
A: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3293
Polymers59,9751
Non-polymers3532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3293
Polymers59,9751
Non-polymers3532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)188.374, 68.075, 89.550
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2237-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 3 - 527 / Label seq-ID: 3 - 527

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-62Y / 3-bromophenyl hydrogen (S)-phenylphosphonate


Mass: 313.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10BrO3P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.39 Å3/Da / Density % sol: 48.59 % / Description: NONE
Crystal growpH: 6.3
Details: 32% PEG 5000 MME, 2 MM (NH4)2SO4, 0.1M MES PH 6.3, 200 MM 62Y PHENOLPHENYLPHOSPHONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.03→66.97 Å / Num. obs: 72479 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8
Reflection shellResolution: 2.03→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

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

1hdh


Resolution: 2.03→93.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.364 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. 2 RESIDUES MISSING FROM N-TERMINUS, 10 RESIDUES MISSING FROM C-TERMINUS RESIDUES 76-84 NOT VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 3641 5 %RANDOM
Rwork0.20663 ---
obs0.20838 68838 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.3 Å2
2--1.69 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.03→93.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 36 665 8849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198410
X-RAY DIFFRACTIONr_bond_other_d0.0040.027790
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.96111446
X-RAY DIFFRACTIONr_angle_other_deg1.044317851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62451030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79822.598408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.466151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7421582
X-RAY DIFFRACTIONr_chiral_restr0.10.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022050
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_it2.0412.3934132
X-RAY DIFFRACTIONr_mcbond_other2.0382.3934131
X-RAY DIFFRACTIONr_mcangle_it3.0313.5795160
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4742.6264278
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 32395 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.027→2.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 257 -
Rwork0.267 5175 -
obs--99.43 %

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