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- PDB-8xx9: Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains -

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Basic information

Entry
Database: PDB / ID: 8xx9
TitleRhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains
Componentsalpha-amylase
KeywordsHYDROLASE / alpha-amylase / (beta/alpha)8 barrel / CARBOHYDRATE
Function / homology:
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 1.4Oct 23, 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

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Assembly

Deposited unit
A: alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9996
Polymers75,3961
Non-polymers6045
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.770, 102.389, 63.397
Angle α, β, γ (deg.)90.00, 96.42, 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: 75395.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DDBJ LC794559
Source: (gene. exp.) Rhodothermus marinus JCM 9785 (bacteria)
Production host: Escherichia coli (E. coli) / References: alpha-amylase

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Non-polymers , 5 types, 494 molecules

#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 1.87 Å3/Da / Density % sol: 34.31 %
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: BL-5A / Wavelength: 1.5 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.55→43.5 Å / Num. obs: 80052 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Net I/σ(I): 22.2
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3709 / Rpim(I) all: 0.212 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17529 3931 4.9 %RANDOM
Rwork0.14839 ---
obs0.14972 76089 99.68 %-
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: 18.366 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.55→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 34 489 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125285
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164767
X-RAY DIFFRACTIONr_angle_refined_deg1.461.6717218
X-RAY DIFFRACTIONr_angle_other_deg0.8371.5810946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.925543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61110784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026389
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021341
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_it1.5111.8252481
X-RAY DIFFRACTIONr_mcbond_other1.5081.8252481
X-RAY DIFFRACTIONr_mcangle_it2.1823.2793100
X-RAY DIFFRACTIONr_mcangle_other2.1843.283101
X-RAY DIFFRACTIONr_scbond_it2.2572.0792804
X-RAY DIFFRACTIONr_scbond_other2.2572.0792805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5093.7144118
X-RAY DIFFRACTIONr_long_range_B_refined4.59722.126087
X-RAY DIFFRACTIONr_long_range_B_other4.55519.955986
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
Rfree0.244 275 -
Rwork0.217 5403 -
obs--96.19 %

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