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- PDB-1uz4: Common inhibition of beta-glucosidase and beta-mannosidase by iso... -

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Basic information

Entry
Database: PDB / ID: 1uz4
TitleCommon inhibition of beta-glucosidase and beta-mannosidase by isofagomine lactam reflects different conformational intineraries for glucoside and mannoside hydrolysis
ComponentsMAN5A
KeywordsHYDROLASE / MANNOSIDASE / INHIBITOR / ISOFAGOMANINELACTAM
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase activity
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCELLVIBRIO MIXTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsVincent, F. / Davies, G.J.
CitationJournal: Chembiochem / Year: 2004
Title: Common Inhibition of Both Beta-Glucosidases and Beta-Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis
Authors: Vincent, F. / Gloster, T.M. / Macdonald, J. / Morland, C. / Stick, R.V. / Dias, F. / Prates, J. / Fontes, C.M.G.A. / Gilbert, H.J. / Davies, G.J.
History
DepositionMar 4, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAN5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7646
Polymers50,2311
Non-polymers5345
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.625, 102.370, 50.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MAN5A / MANNOSIDASE


Mass: 50230.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INHIBITOR ISOFAGOMANINELACTAM / Source: (gene. exp.) CELLVIBRIO MIXTUS (bacteria) / Strain: NCIMB 8633 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6QT42
#2: Chemical ChemComp-IFL / (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE / ISOFAGOMINE LACTAM


Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growpH: 4.6
Details: 24% PEG 4000 0.2M NA ACETATE PH4.6, O.2M AMMONUM SULFATE, pH 4.60

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9761
DetectorDate: Jul 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 49493 / % possible obs: 94.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.28
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.15 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUQ

1uuq


Resolution: 1.71→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.512 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2537 5.1 %RANDOM
Rwork0.133 ---
obs0.135 46919 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.78 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 34 528 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213430
X-RAY DIFFRACTIONr_bond_other_d0.0020.022917
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9214658
X-RAY DIFFRACTIONr_angle_other_deg0.93136794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02726
X-RAY DIFFRACTIONr_nbd_refined0.2090.2720
X-RAY DIFFRACTIONr_nbd_other0.2530.23441
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4050.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8891.52034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61523261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.60331396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1114.51397
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: 1.71→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.214 186
Rwork0.186 3228
Refinement TLS params.Method: refined / Origin x: 71.6277 Å / Origin y: 17.4347 Å / Origin z: 27.3517 Å
111213212223313233
T0.012 Å20.0003 Å20.0005 Å2-0.0004 Å20.002 Å2--0.009 Å2
L0.0742 °2-0.0067 °20.0077 °2-0.0327 °2-0.0188 °2--0.0835 °2
S-0.0002 Å °0.0012 Å °-0.0021 Å °0.0024 Å °0.0026 Å °0.0037 Å °-0.0001 Å °0.0021 Å °-0.0024 Å °

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