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- PDB-4v28: Structure of an E333Q variant of the GH99 endo-alpha-mannanase fr... -

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Basic information

Entry
Database: PDB / ID: 4v28
TitleStructure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with Man-Man-Methylumbelliferone
ComponentsGLYCOSYL HYDROLASE FAMILY 71
KeywordsHYDROLASE / GH99 / CAZY / MANNAN / BACTEROIDES / POLYSACCHARIDE UTILISATION / ENZYME-CARBOHYDRATE INTERACTION / SUBSTRATE COMPLEX
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
3alpha-alpha-mannobiose / 7-hydroxy-4-methyl-2H-chromen-2-one / ACETATE ION / Glycosyl hydrolase family 71
Similarity search - Component
Biological speciesBACTEROIDES XYLANISOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYL HYDROLASE FAMILY 71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2367
Polymers43,4781
Non-polymers7586
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.472, 108.472, 67.803
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-2241-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 43478.281 Da / Num. of mol.: 1 / Mutation: YES
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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 526 molecules

#3: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone


Mass: 176.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsINACTIVE VARIANT E333Q

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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: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE
Crystal growpH: 6.4 / Details: 2.8 M SODIUM ACETATE PH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.2→39.5 Å / Num. obs: 122416 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AD1

4ad1


Resolution: 1.2→76.7 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.818 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.12707 6135 5 %RANDOM
Rwork0.10584 ---
obs0.10691 116080 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 51 521 3379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023103
X-RAY DIFFRACTIONr_bond_other_d0.0020.022766
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9494259
X-RAY DIFFRACTIONr_angle_other_deg1.10836368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94823.129147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8741519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213572
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02778
X-RAY DIFFRACTIONr_nbd_refined0.2890.21269
X-RAY DIFFRACTIONr_nbd_other0.2110.22743
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21512
X-RAY DIFFRACTIONr_nbtor_other0.0890.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1060.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.298
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.291.3581464
X-RAY DIFFRACTIONr_mcbond_other1.2741.3541460
X-RAY DIFFRACTIONr_mcangle_it1.6622.0441836
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0871.5281639
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4882.222407
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.20735869
X-RAY DIFFRACTIONr_sphericity_free41.3185122
X-RAY DIFFRACTIONr_sphericity_bonded9.94856158
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 445 -
Rwork0.217 8504 -
obs--98.82 %

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