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- PDB-6gvb: Crystal structure of Cutibacterium acnes exo-beta-1,4-mannosidase -

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Basic information

Entry
Database: PDB / ID: 6gvb
TitleCrystal structure of Cutibacterium acnes exo-beta-1,4-mannosidase
Componentsexo-beta-1,4-mannosidase
KeywordsHYDROLASE / exo-beta-1 / 4-mannosidase / glycan degradation / enzyme / glycoside hydrolase / family 5
Function / homologyGlycoside hydrolase superfamily / Uncharacterized protein
Function and homology information
Biological speciesCutibacterium acnes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsReichenbach, T. / Divne, C.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research CouncilFORMAS 2013-1741 Sweden
Swedish Research CouncilVR 2013-5717 Sweden
Swedish Research CouncilFORMAS 2012-1513 Sweden
Swedish Research CouncilFORMAS 2014-176 Sweden
CitationJournal: Plos One / Year: 2018
Title: Structural and biochemical characterization of the Cutibacterium acnes exo-beta-1,4-mannosidase that targets the N-glycan core of host glycoproteins.
Authors: Reichenbach, T. / Kalyani, D. / Gandini, R. / Svartstrom, O. / Aspeborg, H. / Divne, C.
History
DepositionJun 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 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: exo-beta-1,4-mannosidase
B: exo-beta-1,4-mannosidase
C: exo-beta-1,4-mannosidase
D: exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,44716
Polymers186,9364
Non-polymers2,51112
Water14,988832
1
A: exo-beta-1,4-mannosidase
B: exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7238
Polymers93,4682
Non-polymers1,2566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint9 kcal/mol
Surface area27880 Å2
MethodPISA
2
C: exo-beta-1,4-mannosidase
D: exo-beta-1,4-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7238
Polymers93,4682
Non-polymers1,2566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint11 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.180, 104.370, 112.750
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
exo-beta-1,4-mannosidase


Mass: 46733.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The residues beyond 395, including the hexahistidine tag, are not visible in the electron density and have therefore not been included in the model.
Source: (gene. exp.) Cutibacterium acnes (bacteria) / Gene: B1B09_09200 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: A0A2B7I7A6
#2: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.76 Å3/Da / Density % sol: 55.44 % / Description: plate shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M MOPS buffer, 0.2 M magnesium acetate, 20% (w/v) PEG 8000 and 5 mM D-mannose 20 mM HEPES pH 7.5, 300 mM NaCl, 10% (v/v)glycerol, 0.5 mM TCEP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 111.07175
SYNCHROTRONSOLEIL PROXIMA 121.03927
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 9, 2017
DECTRIS PILATUS 6M2PIXELFeb 9, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
2channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.071751
21.039271
Reflection

Biso Wilson estimate: 26.7 Å2 / Entry-ID: 6GVB / CC1/2: 0.997

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rrim(I) allRsym valueDiffraction-IDNet I/σ(I)
1.8-49.60117560397.46.80.1210.11119.49
2-48.9821760387.53.30.090.076210.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allRsym valueDiffraction-ID% possible all
1.8-1.96.71.92256150.740.01590.0146196
2-2.12.91.69164990.6290.008460.00692248.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSv1.0data reduction
XSCALEv1.0data scaling
autoSHARP3.10.7phasing
ARP/wARP7.6model building
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.601 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.01
RfactorNum. reflection% reflection
Rfree0.2265 2001 1.14 %
Rwork0.195 --
obs0.1953 175603 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12514 0 156 832 13502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713188
X-RAY DIFFRACTIONf_angle_d0.85918097
X-RAY DIFFRACTIONf_dihedral_angle_d7.42910524
X-RAY DIFFRACTIONf_chiral_restr0.051902
X-RAY DIFFRACTIONf_plane_restr0.0062363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.38181350.364412133X-RAY DIFFRACTION96
1.845-1.89490.39981320.349912220X-RAY DIFFRACTION96
1.8949-1.95060.36271610.305812191X-RAY DIFFRACTION96
1.9506-2.01360.31831240.281312279X-RAY DIFFRACTION97
2.0136-2.08560.34521520.263412266X-RAY DIFFRACTION97
2.0856-2.16910.28491270.238512332X-RAY DIFFRACTION97
2.1691-2.26780.25941390.216412333X-RAY DIFFRACTION97
2.2678-2.38740.26061550.212112376X-RAY DIFFRACTION98
2.3874-2.53690.2591430.210912463X-RAY DIFFRACTION98
2.5369-2.73280.24921460.205812499X-RAY DIFFRACTION98
2.7328-3.00780.28031410.204412562X-RAY DIFFRACTION99
3.0078-3.44290.24221420.189412569X-RAY DIFFRACTION99
3.4429-4.33730.16381530.150512641X-RAY DIFFRACTION99
4.3373-49.620.14631510.143112738X-RAY DIFFRACTION98

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