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- PDB-3wnp: D308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillu... -

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Basic information

Entry
Database: PDB / ID: 3wnp
TitleD308A, F268V, D469Y, A513V, and Y515S quintuple mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoundecaose
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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cycloisomaltooligosaccharide glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSuzuki, R. / Suzuki, N. / Fujimoto, Z. / Momma, M. / Kimura, K. / Kitamura, S. / Kimura, A. / Funane, K.
Citation
Journal: Biochem.J. / Year: 2015
Title: Molecular engineering of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040: structural determinants for the reaction product size and reactivity.
Authors: Suzuki, R. / Suzuki, N. / Fujimoto, Z. / Momma, M. / Kimura, K. / Kitamura, S. / 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_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_asym_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_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cycloisomaltooligosaccharide glucanotransferase
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,17522
Polymers158,1722
Non-polymers3,00320
Water2,972165
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A: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58711
Polymers79,0861
Non-polymers1,50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cycloisomaltooligosaccharide glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58711
Polymers79,0861
Non-polymers1,50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.987, 172.813, 172.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cycloisomaltooligosaccharide glucanotransferase


Mass: 79086.141 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 39-738 / Mutation: D308A, F268V, D469Y, A513V, Y515S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: T-3040 / Gene: cit / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P94286, cycloisomaltooligosaccharide glucanotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 183 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M MES, 10%(v/v) 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→41.85 Å / Num. all: 45817 / Num. obs: 45408 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 60.7 Å2 / Rsym value: 0.089 / Net I/σ(I): 21.3
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2208 / Rsym value: 0.617 / % possible all: 98

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WNN

3wnn


Resolution: 2.8→41.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.275 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24337 2243 5 %RANDOM
Rwork0.18681 ---
obs0.18962 42489 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.987 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2---0.67 Å20 Å2
3---2.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10994 0 178 165 11337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210014
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.93215600
X-RAY DIFFRACTIONr_angle_other_deg0.783322964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5651396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09124.829584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.231151694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1431546
X-RAY DIFFRACTIONr_chiral_restr0.0790.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022854
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 181 -
Rwork0.303 3068 -
obs--96.47 %

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