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- PDB-7ebq: The structural analysis of A.Muciniphila sulfatase -

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Basic information

Entry
Database: PDB / ID: 7ebq
TitleThe structural analysis of A.Muciniphila sulfatase
ComponentsSulfatase
KeywordsHYDROLASE / Akkermansia Muciniphila Sulfatase Mucin
Function / homologyN-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 1. / Sulfatase, conserved site / Alkaline-phosphatase-like, core domain superfamily / hydrolase activity / metal ion binding / Sulfatase
Function and homology information
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBao, R. / Li, C.C. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2016YFA0502700 China
National Natural Science Foundation of China (NSFC)81670008 China
National Natural Science Foundation of China (NSFC)81871615 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural analysis of the sulfatase AmAS from Akkermansia muciniphila.
Authors: Li, C.C. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G. / Tong, A.P. / Tang, H. / Bao, R.
History
DepositionMar 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9893
Polymers60,7281
Non-polymers2612
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.170, 113.469, 164.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

21A-788-

HOH

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Components

#1: Protein Sulfatase


Mass: 60727.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_1074 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2UR15
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.51 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.08M Sodium HEPES, 23% w/v PEG 8000, pH7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→39.44 Å / Num. obs: 30831 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.87 Å2 / Rrim(I) all: 0.222 / Net I/σ(I): 5.16
Reflection shellResolution: 2.3→2.37 Å / Num. unique obs: 3030 / Rrim(I) all: 0.834

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g2v

5g2v


Resolution: 2.4→39.44 Å / SU ML: 0.3461 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1997 8.38 %
Rwork0.2053 21841 -
obs0.2086 23838 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.21 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 16 112 4334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914347
X-RAY DIFFRACTIONf_angle_d1.10255892
X-RAY DIFFRACTIONf_chiral_restr0.0671599
X-RAY DIFFRACTIONf_plane_restr0.006765
X-RAY DIFFRACTIONf_dihedral_angle_d20.09141626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37591400.32811509X-RAY DIFFRACTION96.94
2.46-2.530.35451360.31621539X-RAY DIFFRACTION99.94
2.53-2.60.34621380.30011549X-RAY DIFFRACTION99.53
2.6-2.680.32651400.2851532X-RAY DIFFRACTION99.46
2.68-2.780.28761450.26341536X-RAY DIFFRACTION99.82
2.78-2.890.30881490.2521534X-RAY DIFFRACTION99.7
2.89-3.020.31651300.23631557X-RAY DIFFRACTION99.76
3.02-3.180.27341440.2211545X-RAY DIFFRACTION99.7
3.18-3.380.23921440.19741571X-RAY DIFFRACTION99.83
3.38-3.640.23131460.18671555X-RAY DIFFRACTION99.88
3.64-4.010.19471440.16641568X-RAY DIFFRACTION99.65
4.01-4.590.1691410.1381578X-RAY DIFFRACTION99.83
4.59-5.780.18941440.15921602X-RAY DIFFRACTION100
5.78-39.440.211560.18031666X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: -7.19377293185 Å / Origin y: -3.96787747983 Å / Origin z: 19.6641498323 Å
111213212223313233
T0.100350248592 Å2-0.021429161146 Å2-0.00578792800653 Å2-0.102074946499 Å2-0.00498919473917 Å2--0.137317564216 Å2
L0.393941157448 °2-0.0433624649353 °2-0.279663000467 °2-0.238068477005 °20.0111833391816 °2--1.39038310689 °2
S0.00793625792014 Å °-0.0398451902845 Å °0.00204520063384 Å °-0.0423240253043 Å °-0.0325180453041 Å °0.00241607791738 Å °0.0935677631241 Å °-0.051400205931 Å °-0.00100542126296 Å °
Refinement TLS groupSelection details: all

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