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- PDB-4bok: Crystal structure of Bacillus circulans TN-31 Aman6 -

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Basic information

Entry
Database: PDB / ID: 4bok
TitleCrystal structure of Bacillus circulans TN-31 Aman6
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE
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 ...: / 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
Biological speciesBACILLUS CIRCULANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 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 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: ALPHA-1,6-MANNANASE


Theoretical massNumber of molelcules
Total (without water)38,6531
Polymers38,6531
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.948, 65.093, 90.242
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: 38653.422 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Strain: TN-31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z4P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.94 Å3/Da / Density % sol: 36.45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 19462 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 19.11 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.8
Reflection shellHighest resolution: 2 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.1 / % possible all: 97.1

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.047→40.12 Å / SU ML: 0.06 / σ(F): 1.36 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 997 5.1 %
Rwork0.1702 --
obs0.1727 19461 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.047→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 0 214 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032805
X-RAY DIFFRACTIONf_angle_d0.6793818
X-RAY DIFFRACTIONf_dihedral_angle_d14.482965
X-RAY DIFFRACTIONf_chiral_restr0.053387
X-RAY DIFFRACTIONf_plane_restr0.003499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0474-2.15530.26221520.21382531X-RAY DIFFRACTION98
2.1553-2.29040.27881190.19792603X-RAY DIFFRACTION100
2.2904-2.46720.22241370.17752608X-RAY DIFFRACTION100
2.4672-2.71540.26121490.17572629X-RAY DIFFRACTION100
2.7154-3.10820.22081430.1782637X-RAY DIFFRACTION100
3.1082-3.91550.17551520.14752657X-RAY DIFFRACTION100
3.9155-40.12780.17931450.15832799X-RAY DIFFRACTION100

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