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

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Basic information

Entry
Database: PDB / ID: 4udk
TitleCrystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate
Components(UHGB_MP) x 2
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 / : / 2-acetamido-2-deoxy-alpha-D-glucopyranose / TRIETHYLENE GLYCOL / PHOSPHATE ION / Glycosidase
Similarity search - Component
Biological speciesUNCULTURED ORGANISM (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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)240,10040
Polymers235,9436
Non-polymers4,15834
Water21,6901204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29270 Å2
ΔGint-63 kcal/mol
Surface area60110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.737, 140.886, 168.831
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 , 2 types, 6 molecules ABCDFE

#1: Protein
UHGB_MP


Mass: 39321.422 Da / Num. of mol.: 5
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
#2: Protein UHGB_MP


Mass: 39335.449 Da / Num. of mol.: 1
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-AI
References: UniProt: D9ZDQ9, Transferases; Glycosyltransferases; Hexosyltransferases

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Sugars , 2 types, 12 molecules

#4: 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
#5: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 1226 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1204 / 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: 41.75 % / 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: 1.76→45 Å / Num. obs: 197652 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 9.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.54 / % possible all: 97.8

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Processing

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

4udi


Resolution: 1.76→108.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.449 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAIN ATOMS WERE REMOVED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 9956 5 %RANDOM
Rwork0.15823 ---
obs0.15995 187696 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.76→108.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15385 0 260 1204 16849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01916782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214994
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.94922940
X-RAY DIFFRACTIONr_angle_other_deg0.915334588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04552035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58922.924814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.467152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.95715117
X-RAY DIFFRACTIONr_chiral_restr0.1210.22361
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02119260
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024203
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_it1.3231.4958008
X-RAY DIFFRACTIONr_mcbond_other1.3231.4958007
X-RAY DIFFRACTIONr_mcangle_it1.9182.23410084
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0731.7248774
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: 1.757→1.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 703 -
Rwork0.272 13088 -
obs--94.95 %
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)
10.13150.0332-0.02380.3535-0.01650.08360.00320.0194-0.0075-0.0142-0.0120.0433-0.01380.00450.00870.0260.0049-0.00660.0465-0.00110.041617.190417.4142.2245
20.2981-0.0244-0.0260.17850.01050.1305-0.00150.032400.0093-0.01690.0240.03890.0030.01840.0453-0.0028-0.00230.0235-0.01430.043726.4136-23.30591.9465
30.252-0.02550.01320.3116-0.00680.10690.00230.0254-0.0094-0.0171-0.0114-0.0156-0.00050.01460.00920.01980.00020.00350.05020.00880.037856.99275.02991.6741
40.14-0.1265-0.00450.19720.0090.1849-0.0255-0.0113-0.0230.0637-0.00330.03520.02470.00850.02880.09410.00010.03660.02580.01530.025622.1344-21.24240.3701
50.23540.10050.01490.0901-0.03160.2222-0.0027-0.0247-0.00210.0532-0.00550.0196-0.04140.00370.00820.0965-0.00480.02810.037-0.00760.015121.495220.445840.5342
60.22310.0368-0.13020.3191-0.03890.12120.0018-0.0711-0.02750.0692-0.037-0.0155-0.01320.06140.03520.073-0.0041-0.02020.07090.02550.016957.80740.092739.8995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 2267
2X-RAY DIFFRACTION2B7 - 2234
3X-RAY DIFFRACTION3C7 - 2217
4X-RAY DIFFRACTION4D8 - 2183
5X-RAY DIFFRACTION5E7 - 2171
6X-RAY DIFFRACTION6F8 - 2132

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