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- PDB-6a0l: Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter... -

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Basic information

Entry
Database: PDB / ID: 6a0l
TitleCyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter globiformis, complex with maltose
ComponentsCyclic maltosyl-maltose hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltose / Cyclic maltosyl-maltose hydrolase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKohno, M. / Arakawa, T. / Mori, T. / Nishimoto, T. / Fushinobu, S.
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Structural features of a bacterial cyclic alpha-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis.
Authors: Kohno, M. / Arakawa, T. / Ota, H. / Mori, T. / Nishimoto, T. / Fushinobu, S.
#1: Journal: Biosci. Biotechnol. Biochem. / Year: 2008
Title: Purification and characterization of cyclic maltosyl-(1-->6)-maltose hydrolase and alpha-glucosidase from an Arthrobacter globiformis strain.
Authors: Mori, T. / Nishimoto, T. / Okura, T. / Chaen, H. / Fukuda, S.
#2: Journal: Journal of Applied Glycoscience / Year: 2011
Title: Cloning, Sequencing and Expression of the Genes Encoding Cyclic alpha-Maltosyl-(1-->6)-maltose Hydrolase and alpha-Glucosidase from an Arthrobacter globiformis Strain
Authors: Mori, T. / Nishimoto, T. / Okura, T. / Chaen, H. / Fukuda, S.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Cyclic maltosyl-maltose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0072
Polymers51,6641
Non-polymers3421
Water2,198122
1
A: Cyclic maltosyl-maltose hydrolase
hetero molecules

A: Cyclic maltosyl-maltose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0134
Polymers103,3292
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)47.000, 115.688, 182.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cyclic maltosyl-maltose hydrolase


Mass: 51664.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: cmmF / Production host: Escherichia coli (E. coli) / References: UniProt: D2YYE1
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrte, 0.22 M Ammonium sulfate, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→91.1 Å / Num. obs: 26693 / % possible obs: 88.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 0.115
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 0.022 / Num. unique obs: 25316 / CC1/2: 0.839 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXG

5zxg


Resolution: 2.1→91.1 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.85 / SU B: 9.368 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32341 1344 5 %RANDOM
Rwork0.25222 ---
obs0.25562 25316 84.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→91.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 23 122 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193547
X-RAY DIFFRACTIONr_bond_other_d0.0030.023195
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9324850
X-RAY DIFFRACTIONr_angle_other_deg1.15537316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91323.315178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.21527
X-RAY DIFFRACTIONr_chiral_restr0.1050.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214098
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02877
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_it2.3643.1151755
X-RAY DIFFRACTIONr_mcbond_other2.3633.1131754
X-RAY DIFFRACTIONr_mcangle_it3.5924.6652192
X-RAY DIFFRACTIONr_mcangle_other3.5914.6672193
X-RAY DIFFRACTIONr_scbond_it2.1563.2231792
X-RAY DIFFRACTIONr_scbond_other2.1563.2231792
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3424.7842659
X-RAY DIFFRACTIONr_long_range_B_refined5.43336.7484047
X-RAY DIFFRACTIONr_long_range_B_other5.43336.7514048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 36 -
Rwork0.345 731 -
obs--33.3 %

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