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- PDB-6a0k: Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter... -

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Basic information

Entry
Database: PDB / ID: 6a0k
TitleCyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter globiformis, complex with panose
ComponentsCyclic maltosyl-maltose hydrolase
KeywordsHYDROLASE
Function / homologyOligo-1,6-glucosidase, domain 2 / hydrolase activity, acting on glycosyl bonds / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily / carbohydrate metabolic process / metal ion binding / Cyclic maltosyl-maltose hydrolase
Function and homology information
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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 / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cyclic maltosyl-maltose hydrolase
A: Cyclic maltosyl-maltose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3867
Polymers103,3292
Non-polymers2,0585
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint30 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.293, 180.225, 62.926
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclic maltosyl-maltose hydrolase


Mass: 51664.258 Da / Num. of mol.: 2
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-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate, 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-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.94→90.1 Å / Num. obs: 72961 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 0.137
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 0.024 / Num. unique obs: 69198 / CC1/2: 0.791 / % possible all: 93

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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: 5XZG

5xzg


Resolution: 1.94→90.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.921 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22297 3718 5.1 %RANDOM
Rwork0.18762 ---
obs0.18946 69198 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.505 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.94→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 137 378 7443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197272
X-RAY DIFFRACTIONr_bond_other_d0.0020.026349
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.959961
X-RAY DIFFRACTIONr_angle_other_deg1.172314671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39723.315356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85515992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2581554
X-RAY DIFFRACTIONr_chiral_restr0.1290.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218213
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021593
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_it2.0652.1633566
X-RAY DIFFRACTIONr_mcbond_other2.0652.1633565
X-RAY DIFFRACTIONr_mcangle_it2.9023.2364454
X-RAY DIFFRACTIONr_mcangle_other2.9023.2364455
X-RAY DIFFRACTIONr_scbond_it2.6062.3643706
X-RAY DIFFRACTIONr_scbond_other2.6062.3643706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8853.4835508
X-RAY DIFFRACTIONr_long_range_B_refined5.14326.1598277
X-RAY DIFFRACTIONr_long_range_B_other5.1326.0668227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.943→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 247 -
Rwork0.223 4942 -
obs--96.09 %

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