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- PDB-6kny: Structure of Amuc_1100 without transmembrane region from Akkerman... -

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Basic information

Entry
Database: PDB / ID: 6kny
TitleStructure of Amuc_1100 without transmembrane region from Akkermansia muciniphila
ComponentsProtein Amuc_1100
KeywordsUNKNOWN FUNCTION / Uncharacterized / protein
Function / homology: / membrane / Uncharacterized protein
Function and homology information
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMou, L.Q. / Xiao, Q.J. / Deng, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)YFA052700 China
National Science Foundation (China)JQ007 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of monomeric Amuc_1100 from Akkermansia muciniphila.
Authors: Mou, L. / Peng, X. / Chen, Y. / Xiao, Q. / Liao, H. / Liu, M. / Guo, L. / Liu, Y. / Zhang, X. / Deng, D.
History
DepositionAug 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Amuc_1100
B: Protein Amuc_1100


Theoretical massNumber of molelcules
Total (without water)62,3012
Polymers62,3012
Non-polymers00
Water3,045169
1
A: Protein Amuc_1100


Theoretical massNumber of molelcules
Total (without water)31,1501
Polymers31,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Amuc_1100


Theoretical massNumber of molelcules
Total (without water)31,1501
Polymers31,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein Amuc_1100

A: Protein Amuc_1100

B: Protein Amuc_1100

B: Protein Amuc_1100


Theoretical massNumber of molelcules
Total (without water)124,6014
Polymers124,6014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
Buried area5170 Å2
ΔGint-41 kcal/mol
Surface area34660 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-10 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.504, 119.830, 97.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21B-301-

HOH

31B-400-

HOH

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Components

#1: Protein Protein Amuc_1100


Mass: 31150.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Gene: Amuc_1100 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2UR41
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.81 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium phosphate dibasic, 1.8 M sodium phosphate monobasic, 0.1M sodium phosphate dibasic/citric acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.094→40 Å / Num. obs: 26899 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.99 Å2 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Χ2: 0.546 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.185.80.83426200.7340.3750.9170.41599.7
2.18-2.266.50.67926610.8380.2890.7390.441100
2.26-2.376.60.55526650.8940.2350.6030.464100
2.37-2.496.30.4526460.9130.1950.4910.488100
2.49-2.656.60.32226750.9570.1360.350.516100
2.65-2.856.80.24526800.9690.1020.2660.54100
2.85-3.146.60.17226890.9830.0720.1870.615100
3.14-3.596.50.11226950.9890.0470.1220.725100
3.59-4.526.60.07827260.9930.0330.0850.735100
4.52-406.20.05328420.9970.0230.0580.48499.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.991 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.2066 1998 7.44 %
Rwork0.185 --
obs0.1866 26870 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 34.8405 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 2.1→38.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 0 169 2948
Biso mean---43.24 -
Num. residues----363
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14680.25891300.2602161191
2.1468-2.20480.26751390.24021744100
2.2048-2.26970.25771420.21481769100
2.2697-2.34290.22251410.20731763100
2.3429-2.42660.20471440.19941773100
2.4266-2.52380.23191410.20111760100
2.5238-2.63860.18291420.18841782100
2.6386-2.77770.20331440.19591782100
2.7777-2.95170.19431430.18731775100
2.9517-3.17950.22241420.18081781100
3.1795-3.49930.18071450.16221795100
3.4993-4.00520.18641460.16731814100
4.0052-5.04440.17611450.15541819100
5.0444-38.9910.23771540.20091904100

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