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- PDB-4boj: Crystal structure of Bacillus circulans TN-31 Aman6 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4boj
TitleCrystal structure of Bacillus circulans TN-31 Aman6 in complex with mannobiose
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / OXIDOREDUCTASE
Function / homology
Function and homology information


catalytic activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase ...Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Galactose-binding-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
6alpha-alpha-mannobiose / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.379 Å
AuthorsStriebeck, A. / van Aalten, D.M.F.
CitationJournal: To be Published
Title: The Structure of B. Circulans Aman6 Defines the Fold and Mechanism of the Gh-76 Mannoprotein Transglycosylases and Bacterial Mannosidases
Authors: Striebeck, A. / Borodkin, V.S. / Ferenbach, A.T. / Van Aalten, D.M.F.
History
DepositionMay 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: ALPHA-1,6-MANNANASE
B: ALPHA-1,6-MANNANASE
C: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5616
Polymers116,5343
Non-polymers1,0273
Water19,5641086
1
A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1872
Polymers38,8451
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1872
Polymers38,8451
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1872
Polymers38,8451
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.630, 114.140, 134.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-1,6-MANNANASE / AMAN6


Mass: 38844.648 Da / Num. of mol.: 3 / Fragment: RESIDUES 35-375 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 6-O-ALPHA-D-MANNOPYRANOSYL-D-MANNOPYRANOSE / Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Strain: TN-31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z4P9
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.09 % / Description: NONE
Crystal growDetails: 0.2 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 0.1 M SODIUM CITRATE TRIBASIC DEHYDRATE, PH 4.6, 2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→58 Å / Num. obs: 220511 / % possible obs: 98.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Biso Wilson estimate: 13.59 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9
Reflection shellHighest resolution: 1.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.379→57.912 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 11076 5 %
Rwork0.1705 --
obs0.1715 220506 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.379→57.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8087 0 69 1086 9242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148400
X-RAY DIFFRACTIONf_angle_d1.47811440
X-RAY DIFFRACTIONf_dihedral_angle_d13.3032922
X-RAY DIFFRACTIONf_chiral_restr0.0931181
X-RAY DIFFRACTIONf_plane_restr0.0091481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3793-1.3950.34663480.30266216X-RAY DIFFRACTION90
1.395-1.41140.29363810.28576727X-RAY DIFFRACTION96
1.4114-1.42860.25833840.26026777X-RAY DIFFRACTION98
1.4286-1.44670.25663880.24356897X-RAY DIFFRACTION99
1.4467-1.46570.27583520.22796960X-RAY DIFFRACTION99
1.4657-1.48580.2343540.21636975X-RAY DIFFRACTION100
1.4858-1.5070.22753420.20387051X-RAY DIFFRACTION100
1.507-1.52950.22043530.19256966X-RAY DIFFRACTION100
1.5295-1.55340.22033480.18656963X-RAY DIFFRACTION100
1.5534-1.57890.20583980.18117010X-RAY DIFFRACTION100
1.5789-1.60610.22313390.18377054X-RAY DIFFRACTION100
1.6061-1.63540.21823770.18576952X-RAY DIFFRACTION99
1.6354-1.66680.21683660.17656924X-RAY DIFFRACTION99
1.6668-1.70080.20753810.17957013X-RAY DIFFRACTION100
1.7008-1.73780.22153770.17086985X-RAY DIFFRACTION100
1.7378-1.77820.20363480.17147048X-RAY DIFFRACTION100
1.7782-1.82270.20063770.17077015X-RAY DIFFRACTION100
1.8227-1.8720.20033430.17447042X-RAY DIFFRACTION100
1.872-1.92710.21353870.17636959X-RAY DIFFRACTION99
1.9271-1.98930.18653600.16717006X-RAY DIFFRACTION99
1.9893-2.06040.18863560.16977074X-RAY DIFFRACTION100
2.0604-2.14290.18593830.15857033X-RAY DIFFRACTION100
2.1429-2.24040.17723980.16257018X-RAY DIFFRACTION100
2.2404-2.35860.17913740.16017006X-RAY DIFFRACTION99
2.3586-2.50630.18633670.1666994X-RAY DIFFRACTION99
2.5063-2.69980.19523930.177059X-RAY DIFFRACTION99
2.6998-2.97150.18343770.17497110X-RAY DIFFRACTION99
2.9715-3.40150.17673770.16867075X-RAY DIFFRACTION99
3.4015-4.28530.15673450.13927138X-RAY DIFFRACTION98
4.2853-57.96320.15934030.15077383X-RAY DIFFRACTION99

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