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- PDB-4upi: Dimeric sulfatase SpAS1 from Silicibacter pomeroyi -

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Basic information

Entry
Database: PDB / ID: 4upi
TitleDimeric sulfatase SpAS1 from Silicibacter pomeroyi
ComponentsSULFATASE FAMILY PROTEIN
KeywordsHYDROLASE / SUPERFAMILY / ALKALINE PHOSPHATASE SUPERFAMILY
Function / homology
Function and homology information


sulfuric ester hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfatase family protein
Similarity search - Component
Biological speciesRUEGERIA POMEROYI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsJonas, S. / van Loo, B. / Hollfelder, F. / Hyvonen, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily.
Authors: van Loo, B. / Bayer, C.D. / Fischer, G. / Jonas, S. / Valkov, E. / Mohamed, M.F. / Vorobieva, A. / Dutruel, C. / Hyvonen, M. / Hollfelder, F.
History
DepositionJun 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.2Dec 19, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jan 10, 2024Group: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 2.3Nov 20, 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: SULFATASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4422
Polymers65,3761
Non-polymers651
Water13,836768
1
A: SULFATASE FAMILY PROTEIN
hetero molecules

A: SULFATASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8834
Polymers130,7532
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7430 Å2
ΔGint-20 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.027, 86.029, 82.874
Angle α, β, γ (deg.)90.00, 115.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2145-

HOH

21A-2369-

HOH

31A-2373-

HOH

41A-2374-

HOH

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Components

#1: Protein SULFATASE FAMILY PROTEIN / SULFATASE


Mass: 65376.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FORMYL GLYCINE IN POSITION 77, MODIFIED FROM CYSTEINE, WITH PARTIAL MODIFICATION
Source: (gene. exp.) RUEGERIA POMEROYI (bacteria) / Strain: DSS-3
Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES (DSMZ)
Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LLA5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.3 Å3/Da / Density % sol: 46.51 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL PH 8.0, 20% (W/V) PEG 6000, 0.75 M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.25→74.99 Å / Num. obs: 160317 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 23.378 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.97
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE

1e2s

2vqr

1fsu

1p49

1hth


Resolution: 1.25→37.497 Å / SU ML: 0.1 / σ(F): 1.36 / Phase error: 17.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1631 8048 5 %
Rwork0.1413 --
obs0.1424 160242 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.02 Å2
Refinement stepCycle: LAST / Resolution: 1.25→37.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 1 768 5164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054576
X-RAY DIFFRACTIONf_angle_d1.1236211
X-RAY DIFFRACTIONf_dihedral_angle_d13.5081729
X-RAY DIFFRACTIONf_chiral_restr0.078637
X-RAY DIFFRACTIONf_plane_restr0.006834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.28232400.25574412X-RAY DIFFRACTION85
1.2642-1.27910.25042690.23574665X-RAY DIFFRACTION92
1.2791-1.29470.25892490.25555052X-RAY DIFFRACTION98
1.2947-1.31110.29862670.24925032X-RAY DIFFRACTION99
1.3111-1.32830.22852920.18485112X-RAY DIFFRACTION100
1.3283-1.34650.20662980.17355086X-RAY DIFFRACTION100
1.3465-1.36580.2212690.16975067X-RAY DIFFRACTION100
1.3658-1.38610.19332810.16815140X-RAY DIFFRACTION99
1.3861-1.40780.21812540.16075173X-RAY DIFFRACTION100
1.4078-1.43090.1962610.15985079X-RAY DIFFRACTION100
1.4309-1.45560.17652530.15285151X-RAY DIFFRACTION99
1.4556-1.4820.19632770.14635028X-RAY DIFFRACTION99
1.482-1.51050.17322680.13725155X-RAY DIFFRACTION100
1.5105-1.54140.16892580.12865104X-RAY DIFFRACTION99
1.5414-1.57490.14912740.12495118X-RAY DIFFRACTION99
1.5749-1.61150.14712900.12345078X-RAY DIFFRACTION99
1.6115-1.65180.17682850.11965079X-RAY DIFFRACTION99
1.6518-1.69650.13342880.11935053X-RAY DIFFRACTION99
1.6965-1.74640.14792400.1215125X-RAY DIFFRACTION99
1.7464-1.80280.14662540.13055153X-RAY DIFFRACTION99
1.8028-1.86720.18342700.13715090X-RAY DIFFRACTION99
1.8672-1.9420.16352610.13864998X-RAY DIFFRACTION97
1.942-2.03030.16083000.13375111X-RAY DIFFRACTION99
2.0303-2.13740.14722570.13385113X-RAY DIFFRACTION99
2.1374-2.27130.17412600.14065077X-RAY DIFFRACTION98
2.2713-2.44660.14842630.14335166X-RAY DIFFRACTION100
2.4466-2.69280.18152660.14645135X-RAY DIFFRACTION100
2.6928-3.08220.16062950.1485165X-RAY DIFFRACTION100
3.0822-3.88270.14672550.13655218X-RAY DIFFRACTION100
3.8827-37.51360.15072540.13575259X-RAY DIFFRACTION99

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