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- PDB-3qry: Analysis of a new family of widely distributed metal-independent ... -

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Basic information

Entry
Database: PDB / ID: 3qry
TitleAnalysis of a new family of widely distributed metal-independent alpha mannosidases provides unique insight into the processing of N-linked glycans, Streptococcus pneumoniae SP_2144 1-deoxymannojirimycin complex
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / ALPHA-ALPHA SIX FOLD / GLYCOSIDE HYDROLASE / MANNOSIDASE / 1-DEOXYMANNOJIRIMYCIN
Function / homology
Function and homology information


carbohydrate catabolic process / catalytic activity / carbohydrate metabolic process
Similarity search - Function
Metal-independent alpha-mannosidase / Metal-independent alpha-mannosidase (GH125) / DUF1237 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
1-DEOXYMANNOJIRIMYCIN / Twin-arginine translocation pathway signal / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGregg, K.J. / Zandberg, W.F. / Hehemann, J.-H. / Whitworth, G.E. / Deng, L.E. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Analysis of a New Family of Widely Distributed Metal-independent {alpha}-Mannosidases Provides Unique Insight into the Processing of N-Linked Glycans.
Authors: Gregg, K.J. / Zandberg, W.F. / Hehemann, J.H. / Whitworth, G.E. / Deng, L. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Putative uncharacterized protein
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,91010
Polymers98,2122
Non-polymers6998
Water25,0051388
1
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4555
Polymers49,1061
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4555
Polymers49,1061
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.460, 158.800, 60.040
Angle α, β, γ (deg.)90.00, 107.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 49105.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_2144 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 STAR / References: UniProt: Q97NA8, UniProt: A0A0H2URZ6*PLUS
#2: Chemical ChemComp-DMJ / 1-DEOXYMANNOJIRIMYCIN


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1388 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Hepes, 1.2 M LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 117 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→158.8 Å / Num. all: 88818 / Num. obs: 88818 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.75→1.84 Å / % possible all: 2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.5.0072refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.226 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21845 4679 5 %RANDOM
Rwork0.16959 ---
obs0.17206 88818 97.4 %-
all-88818 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.151 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20.63 Å2
2---0.99 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 46 1388 8356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227164
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9459746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38224.301365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.927151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8161540
X-RAY DIFFRACTIONr_chiral_restr0.0990.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215528
X-RAY DIFFRACTIONr_mcbond_it0.7481.54259
X-RAY DIFFRACTIONr_mcangle_it1.2826890
X-RAY DIFFRACTIONr_scbond_it2.23232905
X-RAY DIFFRACTIONr_scangle_it3.5714.52851
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 303 -
Rwork0.216 5261 -
obs--78.52 %

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