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

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Basic information

Entry
Database: PDB / ID: 4udi
TitleCrystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.85 Angstrom from unknown human gut bacteria (Uhgb_MP)
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
: / TRIETHYLENE GLYCOL / PHOSPHATE ION / Glycosidase
Similarity search - Component
Biological speciesUNCULTURED ORGANISM (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)240,97369
Polymers235,9296
Non-polymers5,04563
Water19,1501063
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33840 Å2
ΔGint-92.1 kcal/mol
Surface area60150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.116, 141.206, 176.245
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 , 1 types, 6 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

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Non-polymers , 6 types, 1126 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 2.22 Å3/Da / Density % sol: 44.66 % / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.96863
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 21, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. obs: 190253 / % possible obs: 98.1 % / Observed criterion σ(I): -1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.46
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.63 / % possible all: 88.7

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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 1VKD

1vkd


Resolution: 1.8→110.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.82 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18993 9557 5 %RANDOM
Rwork0.15537 ---
obs0.1571 180598 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.765 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→110.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15371 0 312 1063 16746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214701
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.94622138
X-RAY DIFFRACTIONr_angle_other_deg0.913333839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85851947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.75222.739785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.353152326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61415117
X-RAY DIFFRACTIONr_chiral_restr0.1190.22263
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024048
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_it1.3751.5737737
X-RAY DIFFRACTIONr_mcbond_other1.3751.5737736
X-RAY DIFFRACTIONr_mcangle_it2.0432.3529677
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0921.8158554
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: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 600 -
Rwork0.325 11106 -
obs--82.64 %
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)
10.8190.0169-0.01630.86550.02810.3579-0.01880.08560.1941-0.04930.01350.1127-0.0251-0.01970.00520.01090.0033-0.0170.01440.0330.417616.635217.45871.6121
20.9981-0.0515-0.04370.7366-0.00650.3622-0.01460.0815-0.1385-0.02740.00610.07120.0673-0.0140.00850.0476-0.00910.00030.0081-0.01560.343526.0019-23.39251.8018
30.8195-0.0847-0.01570.78640.02810.403-0.00540.05330.1176-0.05390.0173-0.17240.00320.0315-0.01190.0049-0.00310.01380.00920.00340.388656.71015.17541.5517
40.9519-0.1347-0.01280.8090.04260.5697-0.0769-0.3421-0.14810.33470.07320.11560.0847-0.04520.00370.1870.03810.07880.13420.09420.281221.5043-21.151340.1386
50.92360.00650.14280.8729-0.07150.6529-0.0906-0.32410.24870.35860.07640.1139-0.0793-0.0680.01410.18940.07750.05170.1407-0.12680.376720.529920.50539.8355
60.8284-0.0338-0.13920.9527-0.04060.6591-0.0743-0.31070.09340.34320.0899-0.22550.01010.1195-0.01570.14530.0712-0.130.1455-0.07020.310757.18160.539640.0779

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