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- PDB-4udj: Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 4udj
TitleCrystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with beta-D-mannopyranose and inorganic phosphate
ComponentsUHGB_MP
KeywordsTRANSFERASE / GLYCOSIDE HYDROLASE FAMILY 130 / B-1 / 4-MANNOPYRANOSYL-CHITOBIOSE PHOSPHORYLASE / N-GLYCAN PHOSPHOROLYSIS
Function / homology
Function and homology information


glycosyltransferase activity
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
beta-D-mannopyranose / : / TRIETHYLENE GLYCOL / PHOSPHATE ION / Glycosidase
Similarity search - Component
Biological speciesUNCULTURED ORGANISM (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLadeveze, S. / Cioci, G. / Potocki-Veronese, G. / Tranier, S. / Mourey, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Bases for N-Glycan Processing by Mannoside Phosphorylase.
Authors: Ladeveze, S. / Cioci, G. / Roblin, P. / Mourey, L. / Tranier, S. / Potocki-Veronese, G.
#1: Journal: J.Biol.Chem. / Year: 2013
Title: Role of Glycoside Phosphorylases in Mannose Foraging by Human Gut Bacteria.
Authors: Ladeveze, S. / Tarquis, L. / Cecchini, D.A. / Bercovici, J. / Andre, I. / Topham, C.M. / Morel, S. / Laville, E. / Monsan, P. / Lombard, V. / Henrissat, B. / Potocki-Veronese, G.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UHGB_MP
B: UHGB_MP
C: UHGB_MP
D: UHGB_MP
E: UHGB_MP
F: UHGB_MP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,92646
Polymers235,9296
Non-polymers3,99840
Water21,1321173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27720 Å2
ΔGint-54.3 kcal/mol
Surface area62840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 140.840, 168.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
UHGB_MP


Mass: 39321.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED ORGANISM (environmental samples)
Description: FECAL SAMPLE FROM HOMO SAPIENS / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI
References: UniProt: D9ZDQ9, Transferases; Glycosyltransferases; Hexosyltransferases
#3: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1207 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1173 / 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: 2.11 Å3/Da / Density % sol: 41.82 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 / Details: PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.94→75 Å / Num. obs: 148390 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UDI

4udi


Resolution: 1.94→108.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.382 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19333 7430 5 %RANDOM
Rwork0.14955 ---
obs0.15173 140869 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.94→108.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15431 0 244 1173 16848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01916802
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215135
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.94722925
X-RAY DIFFRACTIONr_angle_other_deg0.908334889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08452038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.23722.798822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.919152432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.15315125
X-RAY DIFFRACTIONr_chiral_restr0.1210.22334
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024208
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.211.2897990
X-RAY DIFFRACTIONr_mcbond_other1.211.2897989
X-RAY DIFFRACTIONr_mcangle_it1.8691.92510056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.841.5338812
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.937→1.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 551 -
Rwork0.2 10239 -
obs--98.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17130.0329-0.04380.3987-0.01910.09870.01340.0218-0.0004-0.0085-0.01140.0568-0.00670.0107-0.00210.00610.0081-0.00930.0322-0.00140.091817.196917.64642.0164
20.2888-0.001-0.0250.18860.03860.1374-0.01080.03240.00360.0121-0.00790.0330.04270.0170.01870.031-0.00260.00070.0136-0.01190.088826.5078-23.4141.8749
30.2381-0.01190.00070.3211-0.0080.11170.00680.0183-0.0103-0.0166-0.0154-0.0233-0.00350.01150.00860.00140.0040.00320.04170.00970.088357.10245.24351.7247
40.1782-0.117-0.02820.15090.00920.2426-0.0297-0.0005-0.02350.0762-0.00730.04770.03030.01720.0370.09250.00160.05340.01430.01660.050922.0793-21.403740.4411
50.24690.1130.02450.0776-0.03930.22010.0119-0.0223-0.00610.0535-0.01180.0165-0.05940.0004-00.1011-0.00660.04690.0239-0.01440.033621.465520.567240.632
60.24890.0897-0.12310.356-0.05540.12760.0112-0.0786-0.0340.0923-0.0585-0.0287-0.01880.07610.04730.0693-0.0125-0.03260.07430.03830.035858.07510.124340.0187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 2234
2X-RAY DIFFRACTION2B7 - 2239
3X-RAY DIFFRACTION3C8 - 2216
4X-RAY DIFFRACTION4D8 - 2174
5X-RAY DIFFRACTION5E7 - 2190
6X-RAY DIFFRACTION6F8 - 2120

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