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- PDB-5x7g: Crystal Structure of Paenibacillus sp. 598K cycloisomaltooligosac... -

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Basic information

Entry
Database: PDB / ID: 5x7g
TitleCrystal Structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase
ComponentsCycloisomaltooligosaccharide glucanotransferase
KeywordsTRANSFERASE / glydoside hydrolase family 66 / carbohydrate-binding module family 35
Function / homology
Function and homology information


cycloisomaltooligosaccharide glucanotransferase / glycosyltransferase activity / carbohydrate binding / metal ion 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Cycloisomaltooligosaccharide glucanotransferase
Similarity search - Component
Biological speciesPaenibacillus sp. 598K (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFujimoto, Z. / Kishine, N. / Suzuki, N. / Suzuki, R. / Momma, M. / Funane, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
MAFF25001A Japan
Citation
Journal: Biosci. Rep. / Year: 2017
Title: Isomaltooligosaccharide-binding structure ofPaenibacillussp. 598K cycloisomaltooligosaccharide glucanotransferase
Authors: Fujimoto, Z. / Kishine, N. / Suzuki, N. / Suzuki, R. / Mizushima, D. / Momma, M. / Kimura, K. / Funane, K.
#1: Journal: Biochim. Biophys. Acta / Year: 2012
Title: Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K
Authors: Suzuki, R. / Terasawa, K. / Kimura, K. / Fujimoto, Z. / Momma, M. / Kobayashi, M. / Kimura, A. / Funane, K.
History
DepositionFeb 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)81,39611
Polymers80,6191
Non-polymers77810
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-12 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.680, 113.680, 121.635
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-1012-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cycloisomaltooligosaccharide glucanotransferase


Mass: 80618.508 Da / Num. of mol.: 1 / Fragment: UNP residues 41-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. 598K (bacteria) / Strain: 598K / Gene: cit / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: G9MBW2, cycloisomaltooligosaccharide glucanotransferase

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Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% PEG3350, 12% Tacsimate

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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 270 / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 46942 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 33.366 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.021 / Χ2: 1.153 / Net I/σ(I): 32.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4611 / Rpim(I) all: 0.184 / Χ2: 1.316 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WNK

3wnk


Resolution: 2.2→98.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.808 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22164 2388 5.2 %RANDOM
Rwork0.17418 ---
obs0.17666 43870 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.419 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 2.2→98.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 47 289 5877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195743
X-RAY DIFFRACTIONr_bond_other_d0.0020.024794
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9147842
X-RAY DIFFRACTIONr_angle_other_deg0.951311143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0035701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11124.935306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17815824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3931522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
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_it2.8324.5582801
X-RAY DIFFRACTIONr_mcbond_other2.8314.5582800
X-RAY DIFFRACTIONr_mcangle_it4.2366.8253500
X-RAY DIFFRACTIONr_mcangle_other4.2356.8243501
X-RAY DIFFRACTIONr_scbond_it3.1254.8222942
X-RAY DIFFRACTIONr_scbond_other3.1224.8222942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7577.1314342
X-RAY DIFFRACTIONr_long_range_B_refined6.67252.2496396
X-RAY DIFFRACTIONr_long_range_B_other6.6752.1726359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 137 -
Rwork0.254 3203 -
obs--98.85 %

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