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- PDB-4v27: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -

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Basic information

Entry
Database: PDB / ID: 4v27
TitleStructure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / GH99 / CAZY / MANNAN / BACTEROIDES / POLYSACCHARIDE UTILISATION / ENZYME-CARBOHYDRATE INTERACTION / INHIBITOR / GLYCOSIDASE INHIBITION
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / membrane
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / alpha-D-mannopyranose / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHakki, Z. / Bellmaine, S. / Thompson, A.J. / Speciale, G. / Davies, G.J. / Williams, S.J.
CitationJournal: Chemistry / Year: 2015
Title: Structural and Kinetic Dissection of the Endo-Alpha-1,2-Mannanase Activity of Bacterial Gh99 Glycoside Hydrolases from Bacteroides Spp.
Authors: Hakki, Z. / Thompson, A.J. / Bellmaine, S. / Speciale, G. / Davies, G.J. / Williams, S.J.
History
DepositionOct 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 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

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Assembly

Deposited unit
A: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9936
Polymers43,4791
Non-polymers5145
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.280, 108.280, 67.620
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-2179-

HOH

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Components

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


Mass: 43479.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES XYLANISOLVENS (bacteria) / Strain: XB1A / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D6D1V7, glycoprotein endo-alpha-1,2-mannosidase
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: NONE
Crystal growpH: 6.4 / Details: 2.8 M SODIUM ACETATE PH 6.4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.4 Å / Num. obs: 30894 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AD1

4ad1


Resolution: 1.9→38.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.361 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18807 1558 5 %RANDOM
Rwork0.1506 ---
obs0.15245 29317 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.173 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 33 430 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9414040
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63623.264144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9991518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212321
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22037
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8761.522966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4752.2594035
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
Rfree0.238 114 -
Rwork0.204 2092 -
obs--99.95 %

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