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

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Basic information

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


arylsulfatase 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
MALONATE ION / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesPedobacter yulinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 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 1.4Nov 13, 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)51,6397
Polymers51,3921
Non-polymers2476
Water9,998555
1
A: N-acetylgalactosamine-6-sulfatase
hetero molecules

A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,27814
Polymers102,7852
Non-polymers49312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3740 Å2
ΔGint-72 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.620, 83.620, 116.052
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-645-

HOH

21A-1146-

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, 561 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 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: 1.6→40 Å / Num. obs: 59449 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Rsym value: 0.068 / Net I/σ(I): 35.25
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2 / Num. unique obs: 2069 / CC1/2: 0.859 / CC star: 0.961 / Rpim(I) all: 0.186 / Rrim(I) all: 0.487 / Rsym value: 0.449 / % possible all: 67.5

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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: 6UST

6ust


Resolution: 1.603→39.366 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.811 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1779 3033 5.111 %
Rwork0.1476 56312 -
all0.149 --
obs-59345 95.528 %
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: 22.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.348 Å20.174 Å20 Å2
2--0.348 Å2-0 Å2
3----1.129 Å2
Refinement stepCycle: LAST / Resolution: 1.603→39.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 12 555 4068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133624
X-RAY DIFFRACTIONr_bond_other_d0.0350.0153330
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.6514914
X-RAY DIFFRACTIONr_angle_other_deg2.3611.5837675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70622.211199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024197
X-RAY DIFFRACTIONr_gen_planes_other0.020.02879
X-RAY DIFFRACTIONr_nbd_refined0.2230.2760
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.23116
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21800
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2398
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.227
X-RAY DIFFRACTIONr_nbd_other0.2130.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1270.21
X-RAY DIFFRACTIONr_mcbond_it1.4451.5081794
X-RAY DIFFRACTIONr_mcbond_other1.4431.5071793
X-RAY DIFFRACTIONr_mcangle_it2.1562.262246
X-RAY DIFFRACTIONr_mcangle_other2.1562.2612247
X-RAY DIFFRACTIONr_scbond_it2.291.7331830
X-RAY DIFFRACTIONr_scbond_other2.2891.7311827
X-RAY DIFFRACTIONr_scangle_it3.5482.4882668
X-RAY DIFFRACTIONr_scangle_other3.5472.4882669
X-RAY DIFFRACTIONr_lrange_it5.5519.7994390
X-RAY DIFFRACTIONr_lrange_other5.38718.6644236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.603-1.6450.271460.2762969X-RAY DIFFRACTION68.3864
1.645-1.690.2761410.2293409X-RAY DIFFRACTION80.7002
1.69-1.7380.1971870.1883845X-RAY DIFFRACTION93.5716
1.738-1.7920.1862190.1533861X-RAY DIFFRACTION98.2659
1.792-1.850.1852300.1453840X-RAY DIFFRACTION99.706
1.85-1.9150.1892140.1483686X-RAY DIFFRACTION99.8464
1.915-1.9870.1822040.1413594X-RAY DIFFRACTION99.8685
1.987-2.0680.1692060.1423461X-RAY DIFFRACTION99.9727
2.068-2.160.1631830.1423307X-RAY DIFFRACTION99.9714
2.16-2.2650.1561500.1373239X-RAY DIFFRACTION100
2.265-2.3870.1921620.1323034X-RAY DIFFRACTION100
2.387-2.5320.1581730.1362857X-RAY DIFFRACTION99.967
2.532-2.7060.1581620.1372699X-RAY DIFFRACTION99.9651
2.706-2.9210.1611180.142550X-RAY DIFFRACTION99.9625
2.921-3.1980.1761500.1572327X-RAY DIFFRACTION99.7182
3.198-3.5730.171070.1432137X-RAY DIFFRACTION99.8221
3.573-4.120.1661000.1271879X-RAY DIFFRACTION99.5974
4.12-5.0330.167700.131630X-RAY DIFFRACTION99.1832
5.033-7.0620.25770.1821225X-RAY DIFFRACTION96.803
7.062-39.3660.169340.17763X-RAY DIFFRACTION96.3724
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)
10.3569-0.0964-0.00490.52360.02530.4560.0156-0.018-0.0674-0.0911-0.0340.1202-0.0304-0.10020.01840.0290.0166-0.02510.0495-0.00190.04182.6734.47138.765
21.9129-0.371-0.12051.1269-0.3440.9478-0.1159-0.0885-0.5573-0.0468-0.12650.11110.09130.0920.24240.0690.00020.01930.03190.04730.24159.19910.89637.683
30.7623-0.17710.09850.57270.03390.37150.04960.0666-0.0379-0.2038-0.06180.0229-0.0401-0.02450.01220.10340.0316-0.01410.0464-0.00420.004310.61236.19727.989
40.5375-0.1488-0.18940.71950.28420.58480.0398-0.06750.0263-0.09960.0319-0.1372-0.06820.0614-0.07180.03710.00510.03260.03580.00990.040630.51338.37539.817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 196
2X-RAY DIFFRACTION2ALLA197 - 255
3X-RAY DIFFRACTION3ALLA256 - 358
4X-RAY DIFFRACTION4ALLA359 - 445

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