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

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Basic information

Entry
Database: PDB / ID: 7ebp
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 / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Sulfatase
Function and homology information
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80000050381 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 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 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
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7206
Polymers121,4562
Non-polymers2644
Water9,908550
1
A: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8603
Polymers60,7281
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint0 kcal/mol
Surface area20620 Å2
MethodPISA
2
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8603
Polymers60,7281
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.342, 112.722, 165.011
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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 Sulfatase /


Mass: 60727.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_1074 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UR15
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.11M Sodium HEPES, 18% w/v PEG 8000, pH6.5

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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: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.77→39.36 Å / Num. obs: 117585 / % possible obs: 98.4 % / Redundancy: 10 % / Biso Wilson estimate: 19.4404838983 Å2 / Rrim(I) all: 0.104 / Net I/σ(I): 39.1
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 7847 / Rrim(I) all: 0.268

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2V

5g2v


Resolution: 1.80000050381→33.2885624865 Å / SU ML: 0.165023622558 / Cross valid method: FREE R-VALUE / σ(F): 1.45755678847 / Phase error: 19.9741508589
RfactorNum. reflection% reflection
Rfree0.20891334749 5718 5.11943559073 %
Rwork0.186213200819 105974 -
obs0.187402578451 111692 99.9239557333 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8139994501 Å2
Refinement stepCycle: LAST / Resolution: 1.80000050381→33.2885624865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8445 0 14 551 9010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139266545798706
X-RAY DIFFRACTIONf_angle_d1.5172772641111793
X-RAY DIFFRACTIONf_chiral_restr0.09035799487361192
X-RAY DIFFRACTIONf_plane_restr0.007187196871331534
X-RAY DIFFRACTIONf_dihedral_angle_d12.4892275363257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.82050.229867441612020.2155455444493454X-RAY DIFFRACTION99.9726551818
1.8205-1.84190.2356505108352280.2068939589623473X-RAY DIFFRACTION99.8920377868
1.8419-1.86430.2219933282912120.207620638973438X-RAY DIFFRACTION100
1.8643-1.88790.2387847959051940.2062338964053504X-RAY DIFFRACTION100
1.8879-1.91280.2313310574751770.1997741514673503X-RAY DIFFRACTION99.9456816947
1.9128-1.9390.2316075365211800.204031294523511X-RAY DIFFRACTION99.9729144095
1.939-1.96670.2410293497451900.1953259622783501X-RAY DIFFRACTION99.9458434877
1.9667-1.9960.2325160815751660.2046146362323507X-RAY DIFFRACTION99.9183895539
1.996-2.02720.2310263077991940.2074285662563473X-RAY DIFFRACTION100
2.0272-2.06040.2385725855021660.2088891416673568X-RAY DIFFRACTION100
2.0604-2.0960.2320206935711630.1988362308463485X-RAY DIFFRACTION100
2.096-2.13410.2199466398091910.2008483365983546X-RAY DIFFRACTION100
2.1341-2.17510.2338283966611890.2052481480673470X-RAY DIFFRACTION99.9726775956
2.1751-2.21950.2099450254561890.1963230679163551X-RAY DIFFRACTION100
2.2195-2.26770.2214751386971770.1946431606043478X-RAY DIFFRACTION99.9726477024
2.2677-2.32050.2354030921941950.1984254963923528X-RAY DIFFRACTION100
2.3205-2.37850.2213885675072010.2006029245833527X-RAY DIFFRACTION99.973183159
2.3785-2.44280.2072885056072000.1946116141193512X-RAY DIFFRACTION99.9730676003
2.4428-2.51460.2161826450651900.2004031302043505X-RAY DIFFRACTION99.8648648649
2.5146-2.59580.2020032023981780.207149614173554X-RAY DIFFRACTION100
2.5958-2.68850.215255689811970.1981391781443523X-RAY DIFFRACTION100
2.6885-2.79610.2279505333311760.2066123338183564X-RAY DIFFRACTION100
2.7961-2.92330.2383829504941840.1999558985633534X-RAY DIFFRACTION99.9731110514
2.9233-3.07730.2513395947371910.197593402783563X-RAY DIFFRACTION99.9467518637
3.0773-3.270.220061000341870.2002297420843539X-RAY DIFFRACTION99.9731687684
3.27-3.52220.2169372350811910.1835980370943577X-RAY DIFFRACTION99.9734677633
3.5222-3.87610.2011888976091940.163655634753585X-RAY DIFFRACTION100
3.8761-4.43590.1623158818811790.1451943292843621X-RAY DIFFRACTION99.8948475289
4.4359-5.58450.1393728833572350.1408724354933600X-RAY DIFFRACTION99.7918293
5.5845-33.280.2095241694882020.1737901784093780X-RAY DIFFRACTION98.8825428359
Refinement TLS params.Method: refined / Origin x: 24.2924251103 Å / Origin y: 79.9615837619 Å / Origin z: 101.753375979 Å
111213212223313233
T0.142464387519 Å20.0162922866766 Å20.0141835352609 Å2-0.157177444797 Å20.0228053839205 Å2--0.160980077177 Å2
L0.104917639433 °20.157295953561 °20.129041828069 °2-0.270448106392 °20.199102235227 °2--0.223204195554 °2
S0.00202850400599 Å °-0.0108369474532 Å °0.0243373217551 Å °0.0234874881918 Å °-0.0207970034735 Å °0.0347453241085 Å °0.00920892432027 Å °-0.00691663739954 Å °0.0230974082667 Å °
Refinement TLS groupSelection details: all

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