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- PDB-8xxa: Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains... -

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Basic information

Entry
Database: PDB / ID: 8xxa
TitleRhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains in complex with branched pentasaccharide
Componentsalpha-amylase
KeywordsHYDROLASE / alpha-amylase / (beta/alpha)8 barrel / CARBOHYDRATE
Function / homologyalpha-maltotriose / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesRhodothermus marinus JCM 9785 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05956 Japan
CitationJournal: Proteins / Year: 2024
Title: Structural basis for the recognition of alpha-1,6-branched alpha-glucan by GH13_47 alpha-amylase from Rhodothermus marinus.
Authors: Miyasaka, Y. / Yokoyama, K. / Kozono, T. / Kitano, Y. / Miyazaki, T. / Sakaguchi, M. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,50811
Polymers75,3521
Non-polymers2,15610
Water12,827712
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.508, 61.051, 99.808
Angle α, β, γ (deg.)90.00, 106.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein alpha-amylase


Mass: 75351.531 Da / Num. of mol.: 1 / Mutation: D563A
Source method: isolated from a genetically manipulated source
Details: DDBJ accession code LC794559
Source: (gene. exp.) Rhodothermus marinus JCM 9785 (bacteria)
Production host: Escherichia coli (E. coli) / References: alpha-amylase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-6[DGlcpa1-4]DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1_b6-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 720 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES buffer, PEG 20000, PEG 4000, PEG 3350, sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→47.9 Å / Num. obs: 106919 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.032 / Net I/σ(I): 13.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5315 / Rpim(I) all: 0.258 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 5267 4.9 %RANDOM
Rwork0.17361 ---
obs0.17433 101632 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.582 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.55→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 0 139 712 5928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135384
X-RAY DIFFRACTIONr_bond_other_d0.0340.0154831
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6767349
X-RAY DIFFRACTIONr_angle_other_deg2.6051.59511124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82421.281320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8715782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0861543
X-RAY DIFFRACTIONr_chiral_restr0.0810.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026025
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021341
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_it1.1691.7352479
X-RAY DIFFRACTIONr_mcbond_other1.1661.7332478
X-RAY DIFFRACTIONr_mcangle_it1.7562.6013097
X-RAY DIFFRACTIONr_mcangle_other1.7562.6033098
X-RAY DIFFRACTIONr_scbond_it2.051.9782905
X-RAY DIFFRACTIONr_scbond_other2.0491.9782905
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1272.8864253
X-RAY DIFFRACTIONr_long_range_B_refined4.63921.5216338
X-RAY DIFFRACTIONr_long_range_B_other4.41520.7366148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 399 -
Rwork0.21 7523 -
obs--99.66 %

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