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- PDB-4ad2: Structure of the GH99 endo-alpha-mannosidase from Bacteroides xyl... -

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Basic information

Entry
Database: PDB / ID: 4ad2
TitleStructure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-isofagomine
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / ENDOMANNOSIDASE / GLYCOSIDE HYDROLASE GH99 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE GLYCOSIDASE INHIBITION
Function / homology
Function and homology information


alpha-mannosidase activity / membrane
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jul 15, 2015Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYL HYDROLASE FAMILY 71
B: GLYCOSYL HYDROLASE FAMILY 71
C: GLYCOSYL HYDROLASE FAMILY 71
D: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,22612
Polymers173,9174
Non-polymers1,3098
Water24,7531374
1
A: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8073
Polymers43,4791
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8073
Polymers43,4791
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8073
Polymers43,4791
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8073
Polymers43,4791
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)223.296, 223.296, 84.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 43479.266 Da / Num. of mol.: 4
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: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1374 / 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: 3.55 Å3/Da / Density % sol: 65.3 % / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 140911 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG

Resolution: 2.1→44.36 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.349 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21674 7043 5 %RANDOM
Rwork0.18607 ---
obs0.18761 133778 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10953 0 84 1374 12411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.93615648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14651392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81623.12548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.847151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9031570
X-RAY DIFFRACTIONr_chiral_restr0.10.21619
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219033
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25758
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.27815
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.21299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0130.02211465
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3011.93615648
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 508 -
Rwork0.215 9836 -
obs--99.98 %

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