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- PDB-7dsz: Crystal structure of Amuc_1102 from Akkermansia muciniphila -

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Basic information

Entry
Database: PDB / ID: 7dsz
TitleCrystal structure of Amuc_1102 from Akkermansia muciniphila
ComponentsAmuc_1102
KeywordsMOTOR PROTEIN / Akkermansia muciniphila / Amuc_1102 / Type IV pilus / Ig-like fold
Function / homology: / Uncharacterized protein
Function and homology information
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsXiang, R. / Wang, J. / Wang, Y. / Zhang, M. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentKJ2019ZD02 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Amuc_1102 fromAkkermansia muciniphilaadopts animmunoglobulin-like fold related to archaeal type IV pilus
Authors: Xiang, R. / Wang, J. / Xu, W. / Zhang, M. / Wang, M.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amuc_1102
B: Amuc_1102
C: Amuc_1102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3448
Polymers80,1673
Non-polymers1775
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-70 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.469, 83.941, 107.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Amuc_1102


Mass: 26722.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_1102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2UR43
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate, pH 4.6, and 2 M NaCl

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 76720 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.029 / Rrim(I) all: 0.08 / Χ2: 1.005 / Net I/σ(I): 5.6 / Num. measured all: 555345
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.75-1.816.30.82275720.6860.3510.8960.926
1.81-1.897.50.64175660.8250.250.6891.025
1.89-1.977.50.45975950.9080.180.4931.147
1.97-2.077.10.32176060.9430.130.3471.262
2.07-2.27.50.24676080.9670.0960.2651.307
2.2-2.387.50.1876310.9820.070.1941.198
2.38-2.617.10.11276570.9920.0450.1210.937
2.61-2.997.60.07776790.9970.030.0820.884
2.99-3.777.30.04577580.9990.0180.0480.78
3.77-5070.0380480.9990.0120.0330.574

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→25.644 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 3811 4.98 %
Rwork0.1719 72699 -
obs0.1733 76510 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.52 Å2 / Biso mean: 33.629 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.75→25.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 5 643 5314
Biso mean--45.67 39.32 -
Num. residues----568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.75-1.77220.27671310.27042672
1.7722-1.79550.26751360.23682654
1.7955-1.82010.25611330.23842673
1.8201-1.84610.28391450.22722639
1.8461-1.87360.25591180.22042674
1.8736-1.90290.24911220.21372692
1.9029-1.93410.24831310.20612666
1.9341-1.96740.23171200.19712693
1.9674-2.00320.21251590.1832671
2.0032-2.04170.23291550.18832642
2.0417-2.08330.22361420.19352636
2.0833-2.12860.22481490.18512688
2.1286-2.17810.21331620.18592619
2.1781-2.23250.20941640.18112677
2.2325-2.29290.21381560.18242645
2.2929-2.36030.19071220.17612696
2.3603-2.43640.21381380.17782700
2.4364-2.52340.19241440.17912698
2.5234-2.62440.2051420.17792703
2.6244-2.74370.21141370.18462672
2.7437-2.88810.22361540.17982716
2.8881-3.06880.20971540.16972679
3.0688-3.30530.17351650.16052690
3.3053-3.63710.18321240.15462747
3.6371-4.16150.18431280.14482767
4.1615-5.23570.15241340.13322798
5.2357-25.640.19121460.17822892

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