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- PDB-5ayd: Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosacc... -

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Basic information

Entry
Database: PDB / ID: 5ayd
TitleCrystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) in complexes with phosphate
ComponentsBeta-1,4-mannooligosaccharide phosphorylase
KeywordsTRANSFERASE / Glycoside hydrolase family 130
Function / homology
Function and homology information


beta-1,4-mannooligosaccharide phosphorylase / glycosyltransferase activity / cell wall organization / carbohydrate metabolic process
Similarity search - Function
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
PHOSPHATE ION / Beta-1,4-mannooligosaccharide phosphorylase
Similarity search - Component
Biological speciesRuminococcus albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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: Beta-1,4-mannooligosaccharide phosphorylase
B: Beta-1,4-mannooligosaccharide phosphorylase
C: Beta-1,4-mannooligosaccharide phosphorylase
D: Beta-1,4-mannooligosaccharide phosphorylase
E: Beta-1,4-mannooligosaccharide phosphorylase
F: Beta-1,4-mannooligosaccharide phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,68412
Polymers230,1146
Non-polymers5706
Water21,8341212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20050 Å2
ΔGint-120 kcal/mol
Surface area62960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.678, 166.181, 92.969
Angle α, β, γ (deg.)90.00, 118.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-1,4-mannooligosaccharide phosphorylase / RaMP2


Mass: 38352.293 Da / Num. of mol.: 6 / Fragment: UNP residues 1-335
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_0099 / Production host: Escherichia coli (E. coli)
References: UniProt: E6UBR9, beta-1,4-mannooligosaccharide phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium phosphate, 0.1M Tris-HCl buffer, 50%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.76 Å / Num. obs: 109233 / % possible obs: 99.4 % / Redundancy: 3.8 % / Net I/σ(I): 9.75

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata processing
Cootrefinement
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.757 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 5436 5 %
Rwork0.1676 --
obs0.1698 108719 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16200 0 30 1212 17442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816746
X-RAY DIFFRACTIONf_angle_d1.05922782
X-RAY DIFFRACTIONf_dihedral_angle_d13.4915988
X-RAY DIFFRACTIONf_chiral_restr0.0452322
X-RAY DIFFRACTIONf_plane_restr0.0052946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.22961790.21243403X-RAY DIFFRACTION98
2.3261-2.35350.30541800.21683416X-RAY DIFFRACTION100
2.3535-2.38220.28691810.22593443X-RAY DIFFRACTION100
2.3822-2.41240.3031780.22443388X-RAY DIFFRACTION100
2.4124-2.44410.27161840.21093483X-RAY DIFFRACTION100
2.4441-2.47760.26651790.21413415X-RAY DIFFRACTION100
2.4776-2.5130.29361820.21143454X-RAY DIFFRACTION100
2.513-2.55050.26721800.21463424X-RAY DIFFRACTION100
2.5505-2.59030.25431820.20293448X-RAY DIFFRACTION100
2.5903-2.63280.25721790.20713416X-RAY DIFFRACTION100
2.6328-2.67820.27491830.21913452X-RAY DIFFRACTION99
2.6782-2.72690.24851800.20523435X-RAY DIFFRACTION100
2.7269-2.77930.27941810.20283423X-RAY DIFFRACTION100
2.7793-2.8360.23461820.1913457X-RAY DIFFRACTION100
2.836-2.89770.25141830.18483475X-RAY DIFFRACTION100
2.8977-2.96510.2121790.17683406X-RAY DIFFRACTION100
2.9651-3.03920.25031810.1853438X-RAY DIFFRACTION100
3.0392-3.12140.23461820.18023467X-RAY DIFFRACTION100
3.1214-3.21320.21931810.17343437X-RAY DIFFRACTION100
3.2132-3.31690.20541820.16543460X-RAY DIFFRACTION100
3.3169-3.43540.20431800.16343422X-RAY DIFFRACTION100
3.4354-3.57290.19091810.15293436X-RAY DIFFRACTION99
3.5729-3.73540.19351820.15783451X-RAY DIFFRACTION100
3.7354-3.93230.18381800.1473419X-RAY DIFFRACTION99
3.9323-4.17850.16591800.1333432X-RAY DIFFRACTION100
4.1785-4.50080.16811830.12543478X-RAY DIFFRACTION100
4.5008-4.95320.15561820.1283446X-RAY DIFFRACTION100
4.9532-5.66870.17141830.13893473X-RAY DIFFRACTION100
5.6687-7.13730.1821830.14963484X-RAY DIFFRACTION100
7.1373-44.76570.18751840.15293502X-RAY DIFFRACTION100

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