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

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Basic information

Entry
Database: PDB / ID: 5ayc
TitleCrystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) in complexes with sulfate and 4-O-beta-D-mannosyl-D-glucose
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: 1.9 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: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1383
Polymers43,7001
Non-polymers4382
Water8,251458
1
A: 4-O-beta-D-mannosyl-D-glucose phosphorylase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)132,4159
Polymers131,1003
Non-polymers1,3156
Water543
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 area17680 Å2
ΔGint-99 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.700, 87.700, 283.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-852-

HOH

31A-894-

HOH

41A-904-

HOH

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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
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
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: 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: 1.9→50 Å / Num. obs: 33714 / % possible obs: 99.8 % / Redundancy: 11 % / Net I/σ(I): 21.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHENIX(phenix.refine: 1.9_1692)model building
Cootrefinement
XDSdata processing
RefinementResolution: 1.9→39.786 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 1678 4.99 %
Rwork0.1527 --
obs0.1549 33647 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 28 458 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073174
X-RAY DIFFRACTIONf_angle_d1.0734306
X-RAY DIFFRACTIONf_dihedral_angle_d13.5371151
X-RAY DIFFRACTIONf_chiral_restr0.044475
X-RAY DIFFRACTIONf_plane_restr0.005559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.2621300.19742620X-RAY DIFFRACTION100
1.9559-2.0190.22121480.17272626X-RAY DIFFRACTION100
2.019-2.09120.23551190.16122645X-RAY DIFFRACTION100
2.0912-2.17490.20361270.15442633X-RAY DIFFRACTION100
2.1749-2.27390.19361650.15662625X-RAY DIFFRACTION100
2.2739-2.39370.23271390.15572631X-RAY DIFFRACTION100
2.3937-2.54370.21371390.16212650X-RAY DIFFRACTION100
2.5437-2.74010.20951380.16662668X-RAY DIFFRACTION100
2.7401-3.01570.18711430.16042654X-RAY DIFFRACTION100
3.0157-3.45190.1811410.14892677X-RAY DIFFRACTION100
3.4519-4.34810.17581410.1312713X-RAY DIFFRACTION100
4.3481-39.79430.18171480.1452827X-RAY DIFFRACTION100

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