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

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Basic information

Entry
Database: PDB / ID: 7stv
TitleCrystal structure of sulfatase from Pedobacter yulinensis
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE
Function / homologySulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / hydrolase activity / CITRIC ACID / N-acetylgalactosamine-6-sulfatase
Function and homology information
Biological speciesPedobacter yulinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7427
Polymers51,3921
Non-polymers3496
Water2,090116
1
A: N-acetylgalactosamine-6-sulfatase
hetero molecules

A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48314
Polymers102,7852
Non-polymers69812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3360 Å2
ΔGint-70 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.728, 82.728, 115.292
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-505-

CL

21A-700-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 20% w/v polyethylene glycol 3000

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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: 2.34→40 Å / Num. obs: 19275 / % possible obs: 98.8 % / Redundancy: 9.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.048 / Rrim(I) all: 0.148 / Rsym value: 0.101 / Net I/σ(I): 18.5
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2 / Num. unique obs: 936 / CC1/2: 0.948 / CC star: 0.986 / Rpim(I) all: 0.175 / Rrim(I) all: 0.525 / Rsym value: 0.489 / % possible all: 98.7

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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: 2.35→34.232 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.712 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.393 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2295 943 4.904 %
Rwork0.1717 18285 -
all0.174 --
obs-19228 98.353 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 56.402 Å2
Baniso -1Baniso -2Baniso -3
1-2.062 Å21.031 Å20 Å2
2--2.062 Å2-0 Å2
3----6.691 Å2
Refinement stepCycle: LAST / Resolution: 2.35→34.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 18 116 3582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133550
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153245
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6514817
X-RAY DIFFRACTIONr_angle_other_deg1.2711.5827471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86322.256195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26615561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7331523
X-RAY DIFFRACTIONr_chiral_restr0.0590.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024093
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02857
X-RAY DIFFRACTIONr_nbd_refined0.2080.2767
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.23075
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2161
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.221
X-RAY DIFFRACTIONr_nbd_other0.280.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0670.21
X-RAY DIFFRACTIONr_mcbond_it1.7194.831754
X-RAY DIFFRACTIONr_mcbond_other1.7194.8291753
X-RAY DIFFRACTIONr_mcangle_it2.867.2382189
X-RAY DIFFRACTIONr_mcangle_other2.867.2392190
X-RAY DIFFRACTIONr_scbond_it1.8645.0141796
X-RAY DIFFRACTIONr_scbond_other1.8535.0121793
X-RAY DIFFRACTIONr_scangle_it3.1637.4222628
X-RAY DIFFRACTIONr_scangle_other3.1627.4232629
X-RAY DIFFRACTIONr_lrange_it5.18256.3944062
X-RAY DIFFRACTIONr_lrange_other5.18356.3554055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4110.301770.2861236X-RAY DIFFRACTION93.3191
2.411-2.4770.352580.2741336X-RAY DIFFRACTION100
2.477-2.5480.316730.2481253X-RAY DIFFRACTION99.9246
2.548-2.6260.306740.2311235X-RAY DIFFRACTION98.7179
2.626-2.7120.276680.2091190X-RAY DIFFRACTION99.9206
2.712-2.8070.272530.191175X-RAY DIFFRACTION100
2.807-2.9120.279510.1841147X-RAY DIFFRACTION99.9166
2.912-3.030.187670.1741068X-RAY DIFFRACTION100
3.03-3.1640.23500.181055X-RAY DIFFRACTION99.8193
3.164-3.3180.325490.1871002X-RAY DIFFRACTION99.3384
3.318-3.4960.221290.184953X-RAY DIFFRACTION98.4955
3.496-3.7060.208490.158878X-RAY DIFFRACTION97.1698
3.706-3.960.239470.156834X-RAY DIFFRACTION96.4951
3.96-4.2730.145440.132751X-RAY DIFFRACTION94.5303
4.273-4.6760.182370.128702X-RAY DIFFRACTION95.232
4.676-5.2190.252320.138672X-RAY DIFFRACTION98.0501
5.219-6.0090.197320.163599X-RAY DIFFRACTION98.9028
6.009-7.3190.233270.16509X-RAY DIFFRACTION98.893
7.319-10.1810.191220.136422X-RAY DIFFRACTION99.1071
10.181-34.2320.29140.192268X-RAY DIFFRACTION98.1949
Refinement TLS params.Method: refined / Origin x: -33.34 Å / Origin y: 6.47 Å / Origin z: -16.9122 Å
111213212223313233
T0.0866 Å20.0344 Å2-0.0179 Å2-0.0973 Å2-0.0188 Å2--0.0134 Å2
L0.7211 °2-0.1627 °2-0.1402 °2-0.9915 °2-0.3944 °2--0.7423 °2
S-0.135 Å °-0.1441 Å °0.016 Å °0.1245 Å °0.0798 Å °-0.1028 Å °-0.0659 Å °0.0496 Å °0.0553 Å °
Refinement TLS groupSelection: ALL

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