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- PDB-4ad1: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -

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Basic information

Entry
Database: PDB / ID: 4ad1
TitleStructure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION
Function / homologyGlycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / alpha-mannosidase activity / Glycosidases / TIM Barrel / Alpha-Beta Barrel / membrane / Alpha Beta / Glycosyl hydrolase family 71
Function and homology information
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. ...Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stuetz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase.
Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. ...Authors: Thompson, A.J. / Williams, R.J. / Hakki, Z. / Alonzi, D.S. / Wennekes, T. / Gloster, T.M. / Songsrirote, K. / Thomas-Oates, J.E. / Wrodnigg, T.M. / Spreitz, J. / Stutz, A.E. / Butters, T.D. / Williams, S.J. / Davies, G.J.
History
DepositionDec 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3May 1, 2024Group: 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: GLYCOSYL HYDROLASE FAMILY 71


Theoretical massNumber of molelcules
Total (without water)43,4791
Polymers43,4791
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.540, 108.540, 67.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2210-

HOH

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Components

#1: Protein GLYCOSYL HYDROLASE FAMILY 71 / ENDO-ALPHA-MANNOSIDASE


Mass: 43479.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES XYLANISOLVENS (bacteria) / Strain: XB1A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: D6D1V7, glycoprotein endo-alpha-1,2-mannosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.32 Å3/Da / Density % sol: 47.04 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2011 / Details: OSMICS MULTILAYER OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 31100 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Resolution: 1.9→38.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.337 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18549 1569 5 %RANDOM
Rwork0.14951 ---
obs0.15132 29524 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.696 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 0 467 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9324008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57123.264144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.711518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22026
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2405
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0120.0222937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2051.9324008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 114 -
Rwork0.166 2095 -
obs--100 %

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