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- PDB-3wnk: Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligo... -

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Basic information

Entry
Database: PDB / ID: 3wnk
TitleCrystal Structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase
ComponentsCycloisomaltooligosaccharide glucanotransferase
KeywordsTRANSFERASE / C2 type immunoglobulin fold / (beta/alpha)8-barrel / beta-jelly roll / Greek key / Glycoside Hydrolase / alpha-1 / 6-glucan
Function / homology
Function and homology information


cycloisomaltooligosaccharide glucanotransferase / glycosyltransferase activity / carbohydrate binding
Similarity search - Function
Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Carbohydrate binding module (family 35) / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily ...Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / Carbohydrate binding module (family 35) / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycosidases / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Cycloisomaltooligosaccharide glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSuzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Kishine, N. / Suzuki, R. / Kobayashi, M. / Kimura, A. / Funane, K.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase.
Authors: Suzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Kishine, N. / Suzuki, R. / Suzuki, S. / Kitamura, S. / Kobayashi, M. / Kimura, A. / Funane, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization and preliminary X-ray crystallographic analysis of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040.
Authors: Suzuki, N. / Kim, Y.M. / Momma, M. / Fujimoto, Z. / Kobayashi, M. / Kimura, A. / Funane, K.
#2: Journal: Biochim.Biophys.Acta / Year: 2011
Title: Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040.
Authors: Funane, K. / Kawabata, Y. / Suzuki, R. / Kim, Y.M. / Kang, H.K. / Suzuki, N. / Fujimoto, Z. / Kimura, A. / Kobayashi, M.
History
DepositionDec 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,77419
Polymers80,2211
Non-polymers1,55318
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.437, 106.437, 160.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1179-

HOH

21A-1314-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cycloisomaltooligosaccharide glucanotransferase / / CITase


Mass: 80221.305 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: T-3040 / Gene: cit / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P94286, cycloisomaltooligosaccharide glucanotransferase

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Non-polymers , 6 types, 567 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE DEPOSITORS CONFIRM THAT RESIDUE 278 IS PHE AND THAT SWISSPROT IS INCORRECT AT THIS POSITION.

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0M sodium acetate trihydrate, 0.1M HEPES, 0.05M cadmium sulfate hydrate, 12%(v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97800, 0.97885, 0.97931, 0.98319, 0.96408
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 23, 2007 / Details: 1m long bent plane mirror of fused quartz
RadiationMonochromator: Triangular Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.978851
30.979311
40.983191
50.964081
ReflectionResolution: 2.3→44.34 Å / Num. all: 47422 / Num. obs: 47410 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.079 / Net I/σ(I): 47.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 10.6 / Num. unique all: 4667 / Rsym value: 0.423 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→44.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.473 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19203 2396 5.1 %RANDOM
Rwork0.15764 ---
obs0.15938 44946 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.707 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å21.04 Å20 Å2
2--1.04 Å20 Å2
3----3.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.109 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 34 549 6174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195762
X-RAY DIFFRACTIONr_bond_other_d0.0010.025070
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9177840
X-RAY DIFFRACTIONr_angle_other_deg0.724311627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35924.716299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18615864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.861525
X-RAY DIFFRACTIONr_chiral_restr0.0760.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021460
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 175 -
Rwork0.205 3280 -
obs--99.8 %

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