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- PDB-7aj0: Crystal structure of PsFucS1 sulfatase from Pseudoalteromonas sp. -

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Basic information

Entry
Database: PDB / ID: 7aj0
TitleCrystal structure of PsFucS1 sulfatase from Pseudoalteromonas sp.
ComponentsArylsulfatase
KeywordsHYDROLASE / sulfatase Pseudoalteromonas polysaccharide fucoidan fucoidanase exo-acting
Function / homologyAlkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesPseudoalteromonas sp. MB47 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoret, T. / Mikkelsen, M.D. / Czjzek, M. / Meyer, A.S.
CitationJournal: Sci Rep / Year: 2021
Title: A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure.
Authors: Mikkelsen, M.D. / Cao, H.T.T. / Roret, T. / Rhein-Knudsen, N. / Holck, J. / Tran, V.T.T. / Nguyen, T.T. / Tran, V.H.N. / Lezyk, M.J. / Muschiol, J. / Pham, T.D. / Czjzek, M. / Meyer, A.S.
History
DepositionSep 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arylsulfatase
B: Arylsulfatase
C: Arylsulfatase
D: Arylsulfatase
E: Arylsulfatase
F: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,93224
Polymers345,2666
Non-polymers66618
Water23,9601330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The enzyme was analyzed by size-exclusion chromatography using a HiLoad 16/600 Superdex 200 pg column. A single peak with an estimated apparent molecular mass of ~291 kDa ...Evidence: gel filtration, The enzyme was analyzed by size-exclusion chromatography using a HiLoad 16/600 Superdex 200 pg column. A single peak with an estimated apparent molecular mass of ~291 kDa was obtained, suggesting that the quaternary structure in solution is hexameric, in accordance with the quaternary structure observed in the crystal structure of PsFucS1.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29870 Å2
ΔGint-242 kcal/mol
Surface area89050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.198, 182.337, 209.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Arylsulfatase / PsFucS1


Mass: 57544.359 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. MB47 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1330 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6 0.1 M sodium chloride 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→48.34 Å / Num. obs: 115081 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.375 / Rpim(I) all: 0.105 / Rrim(I) all: 0.39 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 14 % / Rmerge(I) obs: 1.985 / Num. unique obs: 78787 / CC1/2: 0.691 / Rpim(I) all: 0.551 / Rrim(I) all: 2.061 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fdj

4fdj


Resolution: 2.5→46.66 Å / SU ML: 0.2996 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 5742 5 %
Rwork0.1716 109191 -
obs0.1735 114933 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23574 0 18 1330 24922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324150
X-RAY DIFFRACTIONf_angle_d0.594632748
X-RAY DIFFRACTIONf_chiral_restr0.0443510
X-RAY DIFFRACTIONf_plane_restr0.00334260
X-RAY DIFFRACTIONf_dihedral_angle_d11.225214466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.29491780.23453629X-RAY DIFFRACTION100
2.53-2.560.26221980.22443566X-RAY DIFFRACTION99.95
2.56-2.590.27751850.22153609X-RAY DIFFRACTION100
2.59-2.620.27241700.22763629X-RAY DIFFRACTION99.92
2.62-2.660.27882280.22833547X-RAY DIFFRACTION100
2.66-2.690.29971900.22043653X-RAY DIFFRACTION99.95
2.69-2.730.25551820.21543568X-RAY DIFFRACTION100
2.73-2.770.26972060.21763613X-RAY DIFFRACTION100
2.77-2.820.26881900.20323540X-RAY DIFFRACTION99.97
2.82-2.860.2792060.2033626X-RAY DIFFRACTION100
2.86-2.910.23571710.19743615X-RAY DIFFRACTION100
2.91-2.960.21881730.19013653X-RAY DIFFRACTION99.95
2.96-3.020.23031960.18923597X-RAY DIFFRACTION99.97
3.02-3.080.22431730.19953628X-RAY DIFFRACTION100
3.08-3.150.23271860.20773618X-RAY DIFFRACTION99.95
3.15-3.220.26171780.20893622X-RAY DIFFRACTION99.97
3.22-3.30.23062000.17623652X-RAY DIFFRACTION100
3.3-3.390.21532030.16883589X-RAY DIFFRACTION99.97
3.39-3.490.17221810.16563637X-RAY DIFFRACTION100
3.49-3.610.20551730.15973673X-RAY DIFFRACTION100
3.61-3.730.18571850.14923630X-RAY DIFFRACTION99.97
3.73-3.880.19262130.14863628X-RAY DIFFRACTION99.95
3.88-4.060.18451850.14113641X-RAY DIFFRACTION100
4.06-4.270.17111980.13533659X-RAY DIFFRACTION100
4.27-4.540.1572140.12443649X-RAY DIFFRACTION99.97
4.54-4.890.15121740.11973688X-RAY DIFFRACTION100
4.89-5.380.18271950.13813704X-RAY DIFFRACTION99.97
5.38-6.160.18471920.16183720X-RAY DIFFRACTION100
6.16-7.760.21322100.17263738X-RAY DIFFRACTION99.97
7.76-46.660.17832090.17513870X-RAY DIFFRACTION98.93
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)
10.444100333760.09482901908440.08516585381040.723623504964-0.1217225092180.6168878116720.00369231260398-0.0181313975564-0.0307133808153-0.0233837896179-0.0377575130917-0.06198642438520.06654899358910.126660914654.2664485945E-60.2375577671950.01409976424640.01159661628670.3196834056570.02088625125580.267160392619-0.442747332747-5.9710289633665.9417047845
20.4875591856790.0687746835671-0.1557792347790.6751714774280.1168641502650.7788660379870.01293053701-0.01796224820220.03403467281240.0168802153670.026537678513-0.0886398595354-0.06930224234240.136668238458.0867906038E-60.289464322887-0.0156600648002-0.002712602658550.284254910421-0.01671692818720.318922376795-7.4951543473930.596535352530.9440107824
30.617189690525-0.158618556377-0.03803621774230.461475118918-0.1568043168961.03522289064-0.009980221320820.06043795554140.0437375379669-0.0511863481725-0.0183874878077-0.0624674619901-0.009574806098980.177625551012-1.29564970288E-50.2942354753590.003823092944810.01150013767860.305815297117-0.005449351140950.2910429072580.996395155523-17.996062006216.2198126255
40.45501384369-0.060853850068-0.03157763471980.856822149978-0.001439317558340.676437353634-0.00623962254402-0.009342721524460.00557441367496-0.02172667075270.003782667189080.118549489707-0.0212598367272-0.08527500276359.87865480881E-60.22660204397-0.009577739437670.002126197795820.280851492087-0.01753871700170.288420883745-39.74709580794.2119945035966.4602953484
50.5489725902130.07942736995130.1352415396430.585269199598-0.1314969785730.76846504046-0.00946278320112-0.0302124251447-0.03555547981890.04888707986150.02628490415830.1049805396730.0913796181643-0.08774114935294.53983797239E-60.317142692992-0.01177641181440.008299251706760.253372366489-0.00822144266740.323580351782-33.686605791-32.541159266431.4371630838
60.507800111907-0.1117163096950.02482670263870.4654651201920.1169473329230.9900531238560.006659778045930.0187441204707-0.0134637598382-0.0548843381986-0.02326401516020.07201544971890.034702178561-0.0874361132958-7.56714463992E-60.2721084092580.00539321315092-0.003387096814720.2948578954140.001581240291880.308659921763-42.230116913515.711332817916.5156621133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 21 through 521)
2X-RAY DIFFRACTION2(chain 'B' and resid 21 through 521)
3X-RAY DIFFRACTION3(chain 'C' and resid 21 through 521)
4X-RAY DIFFRACTION4(chain 'D' and resid 21 through 521)
5X-RAY DIFFRACTION5(chain 'E' and resid 21 through 521)
6X-RAY DIFFRACTION6(chain 'F' and resid 21 through 521)

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