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- PDB-6lad: Crystal structure of Amuc_1100 from Akkermansia muciniphila -

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Basic information

Entry
Database: PDB / ID: 6lad
TitleCrystal structure 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: 2.7 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
C: Amuc_1100
D: Amuc_1100
E: Amuc_1100
F: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)194,1166
Polymers194,1166
Non-polymers00
Water2,972165
1
A: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)32,3531
Polymers32,3531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Amuc_1100
B: Amuc_1100
C: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)97,0583
Polymers97,0583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-28 kcal/mol
Surface area27350 Å2
MethodPISA
8
D: Amuc_1100
E: Amuc_1100
F: Amuc_1100


Theoretical massNumber of molelcules
Total (without water)97,0583
Polymers97,0583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-28 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.657, 123.560, 131.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))
21(chain B and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))
31(chain C and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))
41(chain D and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))
51(chain E and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))
61(chain F and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))

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 64 through 185 or resid 198 through 239 or resid 294 through 309))AA64 - 18535 - 156
12ALAALAARGARG(chain A and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))AA198 - 239169 - 210
13GLNGLNPROPRO(chain A and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))AA294 - 309265 - 280
21SERSERPROPRO(chain B and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))BB64 - 18535 - 156
22ALAALAARGARG(chain B and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))BB198 - 239169 - 210
23GLNGLNPROPRO(chain B and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))BB294 - 309265 - 280
31SERSERPROPRO(chain C and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))CC64 - 18535 - 156
32ALAALAARGARG(chain C and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))CC198 - 239169 - 210
33GLNGLNPROPRO(chain C and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))CC294 - 309265 - 280
41SERSERPROPRO(chain D and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))DD64 - 18535 - 156
42ALAALAARGARG(chain D and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))DD198 - 239169 - 210
43GLNGLNPROPRO(chain D and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))DD294 - 309265 - 280
51SERSERPROPRO(chain E and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))EE64 - 18535 - 156
52ALAALAARGARG(chain E and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))EE198 - 239169 - 210
53GLNGLNPROPRO(chain E and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))EE294 - 309265 - 280
61SERSERPROPRO(chain F and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))FF64 - 18535 - 156
62ALAALAARGARG(chain F and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))FF198 - 239169 - 210
63GLNGLNPROPRO(chain F and (resid 64 through 185 or resid 198 through 239 or resid 294 through 309))FF294 - 309265 - 280

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Components

#1: Protein
Amuc_1100


Mass: 32352.695 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl, pH 8.0, 40% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 51987 / % possible obs: 98.6 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Χ2: 0.901 / Net I/σ(I): 11.7 / Num. measured all: 523303
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.810.20.85651570.8620.2780.9010.88999.6
2.8-2.9110.20.53151940.9390.1730.560.88399.5
2.91-3.0410.10.38451480.9630.1260.4050.87899.4
3.04-3.29.90.24451070.9850.0810.2570.89597.9
3.2-3.49.90.14750890.9940.0490.1550.89597.2
3.4-3.6610.60.09751860.9970.0310.1020.999.3
3.66-4.0310.30.06852250.9980.0220.0720.89699.3
4.03-4.629.90.0552070.9990.0160.0520.87998.3
4.62-5.819.90.04152280.9990.0140.0430.92198
5.81-509.70.03254460.9990.0110.0340.97498.1

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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: 2.7→48.933 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2813 5.42 %
Rwork0.213 49126 -
obs0.215 51939 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.04 Å2 / Biso mean: 62.2549 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: final / Resolution: 2.7→48.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8897 0 0 165 9062
Biso mean---50.14 -
Num. residues----1133
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5241X-RAY DIFFRACTION7.742TORSIONAL
12B5241X-RAY DIFFRACTION7.742TORSIONAL
13C5241X-RAY DIFFRACTION7.742TORSIONAL
14D5241X-RAY DIFFRACTION7.742TORSIONAL
15E5241X-RAY DIFFRACTION7.742TORSIONAL
16F5241X-RAY DIFFRACTION7.742TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7004-2.7470.38721380.3345242699
2.747-2.79690.32791020.3037247199
2.7969-2.85070.28761390.2723245199
2.8507-2.90890.32491410.2718246199
2.9089-2.97220.29451340.2806246799
2.9722-3.04130.27861320.2832242299
3.0413-3.11730.34491400.2738240998
3.1173-3.20160.29641410.2677241598
3.2016-3.29580.27321210.2605237095
3.2958-3.40210.31051360.2513245599
3.4021-3.52370.27671540.2409244899
3.5237-3.66470.28091270.2312246199
3.6647-3.83150.27581610.2207245699
3.8315-4.03340.26091660.2158244099
4.0334-4.2860.23821560.196246999
4.286-4.61660.20011150.169246798
4.6166-5.08080.1791060.1588244096
5.0808-5.8150.21691560.18382520100
5.815-7.32230.22381830.1906250299
7.3223-48.930.20411650.1718257697

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