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- PDB-6laf: Crystal structure of the core domain of Amuc_1100 from Akkermansi... -

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Basic information

Entry
Database: PDB / ID: 6laf
TitleCrystal structure of the core domain of Amuc_1100 from Akkermansia muciniphila
ComponentsAmuc_1100
KeywordsMEMBRANE PROTEIN / Akkermansia muciniphila / outer-membrane protein / Amuc_1100 / type II Secretion System / toll-like receptor 2
Function / homology: / membrane / Uncharacterized protein
Function and homology information
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsWang, J. / Xiang, R. / Zhang, M. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: J.Struct.Biol. / Year: 2020
Title: The variable oligomeric state of Amuc_1100 from Akkermansia muciniphila.
Authors: Wang, J. / Xiang, R. / Wang, R. / Zhang, B. / Gong, W. / Zhang, J. / Zhang, M. / Wang, M.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 3, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amuc_1100
B: Amuc_1100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2257
Polymers53,7452
Non-polymers4805
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-13 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.746, 85.538, 86.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21B-402-

SO4

31A-504-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 81 through 185 or resid 197 through 308))
21(chain B and (resid 81 through 245 or resid 293 through 308))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain A and (resid 81 through 185 or resid 197 through 308))AA81 - 1852 - 106
12GLNGLNGLNGLN(chain A and (resid 81 through 185 or resid 197 through 308))AA197 - 308118 - 229
21SERSERPROPRO(chain B and (resid 81 through 245 or resid 293 through 308))BB81 - 2452 - 166
22GLUGLUGLNGLN(chain B and (resid 81 through 245 or resid 293 through 308))BB293 - 308214 - 229

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Components

#1: Protein Amuc_1100


Mass: 26872.518 Da / Num. of mol.: 2
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_1100 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: B2UR41
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2 M AmSO4

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9314 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.088 / Rrim(I) all: 0.283 / Χ2: 1.209 / Net I/σ(I): 3.2 / Num. measured all: 96539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.1111.31.4588920.8490.4531.5280.872100
3.11-3.2311.21.0459100.8180.3251.0960.908100
3.23-3.38110.8229250.9120.2580.8631.025100
3.38-3.569.90.8139040.9240.2730.8592.14999.9
3.56-3.789.50.5319230.9520.1850.5641.91799.9
3.78-4.079.60.4329170.9450.1530.461.95799.6
4.07-4.4811.20.1639250.9930.0510.1710.946100
4.48-5.1310.50.1219380.9950.0390.1270.869100
5.13-6.4610.20.129560.9950.0390.1270.884100
6.46-509.50.06210240.9980.0210.0660.84599.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.001→21.603 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2978 438 4.76 %
Rwork0.2569 8769 -
obs0.2588 9207 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.73 Å2 / Biso mean: 59.4009 Å2 / Biso min: 33.05 Å2
Refinement stepCycle: final / Resolution: 3.001→21.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 25 6 2845
Biso mean--68.5 43.73 -
Num. residues----358
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1554X-RAY DIFFRACTION11.863TORSIONAL
12B1554X-RAY DIFFRACTION11.863TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.001-3.43360.40481360.3563286099
3.4336-4.32030.31871560.293286598
4.3203-21.6030.24441460.20033044100

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