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- PDB-7stu: Crystal structure of sulfatase from Pedobacter yulinensis -

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Basic information

Entry
Database: PDB / ID: 7stu
TitleCrystal structure of sulfatase from Pedobacter yulinensis
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
BROMIDE ION / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesPedobacter yulinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsO'Malley, A. / Schlachter, C.R. / Grimes, L.L. / Tomashek, J.J. / Lee, A.L. / Chruszcz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2021
Title: Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis .
Authors: Schlachter, C.R. / O'Malley, A. / Grimes, L.L. / Tomashek, J.J. / Chruszcz, M. / Lee, L.A.
History
DepositionNov 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,90110
Polymers51,3921
Non-polymers5099
Water5,693316
1
A: N-acetylgalactosamine-6-sulfatase
hetero molecules

A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,80220
Polymers102,7852
Non-polymers1,01718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)83.286, 83.286, 115.793
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-846-

HOH

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Components

#1: Protein N-acetylgalactosamine-6-sulfatase


Mass: 51392.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter yulinensis (bacteria) / Gene: C7T94_09545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T3HKC0
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.15 M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→40 Å / Num. obs: 23149 / % possible obs: 99.2 % / Redundancy: 9.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.057 / Rrim(I) all: 0.172 / Rsym value: 0.128 / Net I/σ(I): 15.14
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2 / Num. unique obs: 1144 / CC1/2: 0.738 / CC star: 0.922 / Rpim(I) all: 0.339 / Rrim(I) all: 0.858 / Rsym value: 0.907 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7STT

7stt


Resolution: 2.23→39.217 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.177 / SU ML: 0.164 / Cross valid method: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.215
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2252 1205 5.235 %
Rwork0.1738 21815 -
all0.176 --
obs-23020 99.19 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20.565 Å20 Å2
2--1.13 Å2-0 Å2
3----3.664 Å2
Refinement stepCycle: LAST / Resolution: 2.23→39.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 9 316 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133586
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153292
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.654862
X-RAY DIFFRACTIONr_angle_other_deg1.3311.5837583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01422.335197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5441523
X-RAY DIFFRACTIONr_chiral_restr0.0640.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
X-RAY DIFFRACTIONr_nbd_refined0.2090.2811
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23191
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2307
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.223
X-RAY DIFFRACTIONr_nbd_other0.1960.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2360.21
X-RAY DIFFRACTIONr_mcbond_it1.0422.4861779
X-RAY DIFFRACTIONr_mcbond_other1.0392.4851778
X-RAY DIFFRACTIONr_mcangle_it1.8313.7262222
X-RAY DIFFRACTIONr_mcangle_other1.8313.7282223
X-RAY DIFFRACTIONr_scbond_it1.1052.581807
X-RAY DIFFRACTIONr_scbond_other1.1052.5811808
X-RAY DIFFRACTIONr_scangle_it1.9013.8112640
X-RAY DIFFRACTIONr_scangle_other1.9013.8112640
X-RAY DIFFRACTIONr_lrange_it6.2930.6024299
X-RAY DIFFRACTIONr_lrange_other6.13430.0584245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.2880.3191020.2821553X-RAY DIFFRACTION99.3397
2.288-2.350.308780.2181560X-RAY DIFFRACTION99.7564
2.35-2.4180.226810.1951523X-RAY DIFFRACTION99.442
2.418-2.4920.2511010.1721440X-RAY DIFFRACTION99.8704
2.492-2.5740.22660.1751424X-RAY DIFFRACTION98.6755
2.574-2.6640.186740.1641375X-RAY DIFFRACTION99.8622
2.664-2.7640.204770.1711348X-RAY DIFFRACTION99.7899
2.764-2.8760.238770.1681269X-RAY DIFFRACTION100
2.876-3.0030.24790.1711234X-RAY DIFFRACTION99.9239
3.003-3.1490.249490.1811200X-RAY DIFFRACTION100
3.149-3.3180.242640.191145X-RAY DIFFRACTION100
3.318-3.5180.226610.1891042X-RAY DIFFRACTION98.6583
3.518-3.7590.25520.173986X-RAY DIFFRACTION96.9188
3.759-4.0570.209380.151940X-RAY DIFFRACTION97.1202
4.057-4.4390.197380.14860X-RAY DIFFRACTION97.1861
4.439-4.9560.233400.145800X-RAY DIFFRACTION98.476
4.956-5.7080.143300.167719X-RAY DIFFRACTION99.8667
5.708-6.9550.239350.164616X-RAY DIFFRACTION100
6.955-9.6910.193470.153461X-RAY DIFFRACTION97.6923
9.691-39.2170.175150.193312X-RAY DIFFRACTION99.6951
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59280.0821-0.12890.47380.08210.53640.02740.0725-0.10760.0271-0.0351-0.01930.0679-0.04290.00780.0948-0.0163-0.01840.1043-0.02530.0241-27.022418.689619.3851
23.11670.66021.13570.91140.0231.0701-0.02110.0511-0.37390.0115-0.0762-0.33010.04740.01260.09730.14460.0199-0.03090.1274-0.00740.2025-6.450414.171616.48
31.40970.71960.70830.77430.37910.9707-0.01770.13950.0267-0.0748-0.0224-0.01750.0239-0.07180.04010.0925-0.00530.00010.1647-0.00620.0058-24.793627.3529.676
41.1359-0.0284-0.02880.7650.01810.65490.09210.0470.1336-0.0052-0.0473-0.0804-0.097-0.0151-0.04480.08780.00470.00580.09490.01960.0285-19.757343.949418.0476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 209
2X-RAY DIFFRACTION2ALLA210 - 260
3X-RAY DIFFRACTION3ALLA261 - 344
4X-RAY DIFFRACTION4ALLA345 - 445

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