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- PDB-5ndx: The bacterial orthologue of Human a-L-iduronidase does not need N... -

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Basic information

Entry
Database: PDB / ID: 5ndx
TitleThe bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I
ComponentsGlycosyl hydrolase
KeywordsHYDROLASE / Human a-L-iduronidase / Mucopolysaccharidosis I / Catalytic itinerary / Reaction coordinates / Catalytic mechanism / N-glycosylation site / Rhizobium leguminosarum / Iduronidase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 39 / : / Glycosyl hydrolases family 39 / : / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8U8 / Glyosyl hydrolase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRaich, L. / Valero-Gonzalez, J. / Castro-Lopez, J. / Millan, C. / Jimenez-Garcia, M.J. / Nieto, P. / Uson, I. / Hurtado-Guerrero, R. / Rovira, C.
Funding support Spain, 3items
OrganizationGrant numberCountry
MICINNCTQ2013-44367-C2-2-P Spain
MICINNBFU2016-75633-P Spain
MICINNCTQ2014-55174 Spain
CitationJournal: To Be Published
Title: The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I.
Authors: Raich, L. / Valero-Gonzalez, J. / Castro-Lopez, J. / Millan, C. / Jimenez-Garcia, M.J. / Nieto, P. / Uson, I. / Hurtado-Guerrero, R. / Rovira, C.
History
DepositionMar 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64014
Polymers68,8791
Non-polymers1,76113
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-115 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.028, 173.028, 156.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-702-

SO4

21A-702-

SO4

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Components

#1: Protein Glycosyl hydrolase / Iduronidase


Mass: 68879.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This enzyme is the inactive mutant Glu146Gln of Rhizobium leguminosarum Iduronidase
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: BAE36_24485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8R7L2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8U8 / (2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid


Mass: 352.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1 M succinic acid, 1% PEG 2000 MME and 100 mM HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 70222 / % possible obs: 99.9 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.013 / Net I/σ(I): 38.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.6 / Rpim(I) all: 0.137 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: See our manuscript for the template

Resolution: 2.2→149.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.414 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17499 1939 2.8 %RANDOM
Rwork0.15865 ---
obs0.15913 68241 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.533 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.53 Å20 Å2
2---1.05 Å20 Å2
3---3.41 Å2
Refinement stepCycle: 1 / Resolution: 2.2→149.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 105 384 5210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194974
X-RAY DIFFRACTIONr_bond_other_d0.0020.024603
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9866789
X-RAY DIFFRACTIONr_angle_other_deg1.083.00310600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.355614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12222.636220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49615767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3731546
X-RAY DIFFRACTIONr_chiral_restr0.1150.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021134
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_it2.3723.5932432
X-RAY DIFFRACTIONr_mcbond_other2.3663.5912431
X-RAY DIFFRACTIONr_mcangle_it3.765.3733039
X-RAY DIFFRACTIONr_mcangle_other3.765.3753040
X-RAY DIFFRACTIONr_scbond_it3.0714.0682540
X-RAY DIFFRACTIONr_scbond_other3.0714.0682540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.795.9813742
X-RAY DIFFRACTIONr_long_range_B_refined8.52844.6565689
X-RAY DIFFRACTIONr_long_range_B_other8.52844.6485687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 124 -
Rwork0.19 4984 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.8043 Å / Origin y: 74.0566 Å / Origin z: 1.1474 Å
111213212223313233
T0.0201 Å20.0063 Å20.0092 Å2-0.1539 Å20.0264 Å2--0.0503 Å2
L0.5603 °2-0.0538 °2-0.1662 °2-0.0852 °2-0.0022 °2--0.0732 °2
S0.0009 Å °-0.1161 Å °-0.0143 Å °-0.04 Å °0.0083 Å °-0.0168 Å °0.007 Å °-0.0132 Å °-0.0092 Å °

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