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- PDB-5ay9: Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glu... -

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Basic information

Entry
Database: PDB / ID: 5ay9
TitleCrystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)
Components4-O-beta-D-mannosyl-D-glucose phosphorylase
KeywordsTRANSFERASE / Glycoside hydrolase family 130
Function / homology
Function and homology information


4-O-beta-D-mannosyl-D-glucose phosphorylase / hexosyltransferase activity / cell wall organization / carbohydrate metabolic process
Similarity search - Function
4-O-beta-D-mannosyl-D-glucose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
4-O-beta-D-mannosyl-D-glucose phosphorylase
Similarity search - Component
Biological speciesRuminococcus albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYe, Y. / Saburi, W. / Kato, K. / Yao, M.
CitationJournal: Febs Lett. / Year: 2016
Title: Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies
Authors: Ye, Y. / Saburi, W. / Odaka, R. / Kato, K. / Sakurai, N. / Komoda, K. / Nishimoto, M. / Kitaoka, M. / Mori, H. / Yao, M.
History
DepositionAug 11, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 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: 4-O-beta-D-mannosyl-D-glucose phosphorylase


Theoretical massNumber of molelcules
Total (without water)43,7001
Polymers43,7001
Non-polymers00
Water00
1
A: 4-O-beta-D-mannosyl-D-glucose phosphorylase

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase

A: 4-O-beta-D-mannosyl-D-glucose phosphorylase


Theoretical massNumber of molelcules
Total (without water)131,1003
Polymers131,1003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14150 Å2
ΔGint-63 kcal/mol
Surface area41880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.900, 88.900, 286.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 4-O-beta-D-mannosyl-D-glucose phosphorylase / Mannosylglucose phosphorylase / RaMP1


Mass: 43700.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus albus (strain ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7) (bacteria)
Strain: ATCC 27210 / DSM 20455 / JCM 14654 / NCDO 2250 / 7 / Gene: Rumal_0852 / Production host: Escherichia coli (E. coli)
References: UniProt: E6UIS7, 4-O-beta-D-mannosyl-D-glucose phosphorylase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium nitrate, 0.1M Bis-Tris propane buffer, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.01 Å / Num. obs: 15552 / % possible obs: 99.3 % / Redundancy: 9.1 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
RefinementResolution: 2.5→46.003 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 776 5 %
Rwork0.2389 --
obs0.2409 15516 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3059 0 0 0 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053126
X-RAY DIFFRACTIONf_angle_d1.0524242
X-RAY DIFFRACTIONf_dihedral_angle_d17.0851140
X-RAY DIFFRACTIONf_chiral_restr0.044464
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.38291280.33582415X-RAY DIFFRACTION100
2.6566-2.86170.36021290.30262452X-RAY DIFFRACTION100
2.8617-3.14970.36111270.292404X-RAY DIFFRACTION100
3.1497-3.60530.31371280.24862452X-RAY DIFFRACTION100
3.6053-4.54160.24311300.21722464X-RAY DIFFRACTION100
4.5416-46.0110.22881340.19922553X-RAY DIFFRACTION99

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