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- PDB-9us5: Domain N deletion mutant of Klebsiella pneumoniae maltohexaose-pr... -

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Basic information

Entry
Database: PDB / ID: 9us5
TitleDomain N deletion mutant of Klebsiella pneumoniae maltohexaose-producing alpha-amylase in complex with maltohexaose
ComponentsMaltohexaose-producing amylase
KeywordsHYDROLASE / glycosyl hydrolase family 13
Function / homology
Function and homology information


glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / alpha-glucan catabolic process / alpha-amylase activity / oligosaccharide catabolic process / periplasmic space / calcium ion binding
Similarity search - Function
Alpha-amylase, MalS type / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltotetraose / Maltohexaose-producing amylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsFujimoto, Z. / Kishine, N. / Momma, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Biochem. / Year: 2025
Title: Crystal structure of Klebsiella pneumoniae maltohexaose-producing alpha-amylase.
Authors: Fujimoto, Z. / Kishine, N. / Momma, M.
#1: Journal: Acta Crystallogr D Biol Crystallogr. / Year: 2004
Title: Expression, crystallization and preliminary X-ray crystallographic studies of Klebsiella pneumoniae maltohexaose-producing alpha-amylase.
Authors: Momma, M. / Fujimoto, Z.
History
DepositionMay 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltohexaose-producing amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5444
Polymers63,7971
Non-polymers7473
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-1 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.084, 163.084, 139.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-839-

HOH

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Components

#1: Protein Maltohexaose-producing amylase


Mass: 63797.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli B (bacteria) / Strain (production host): B834(DE3)
References: UniProt: Q9RHR1, glucan 1,4-alpha-maltohexaosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 3.0~3.2 M NaCl 1 mM CaCl2 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→100 Å / Num. obs: 27247 / % possible obs: 100 % / Redundancy: 26.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 29.3
Reflection shellResolution: 2.66→2.8 Å / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3935

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9US3

9us3


Resolution: 2.66→43.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.21 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2259 1362 5 %
Rwork0.1818 25880 -
all0.184 --
obs-27242 99.919 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20 Å2-0 Å2
2--0.024 Å2-0 Å2
3----0.047 Å2
Refinement stepCycle: LAST / Resolution: 2.66→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 47 84 4561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154113
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.6536260
X-RAY DIFFRACTIONr_angle_other_deg1.141.5999480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9815557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39522.869251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69815719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6171523
X-RAY DIFFRACTIONr_chiral_restr0.0440.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021135
X-RAY DIFFRACTIONr_nbd_refined0.1820.2911
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.23936
X-RAY DIFFRACTIONr_nbtor_refined0.160.22185
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2130
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0420.25
X-RAY DIFFRACTIONr_nbd_other0.1730.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.24
X-RAY DIFFRACTIONr_mcbond_it2.9197.3632231
X-RAY DIFFRACTIONr_mcbond_other2.9187.3592230
X-RAY DIFFRACTIONr_mcangle_it4.63311.042787
X-RAY DIFFRACTIONr_mcangle_other4.63311.0442788
X-RAY DIFFRACTIONr_scbond_it3.0267.7072378
X-RAY DIFFRACTIONr_scbond_other3.0147.7072378
X-RAY DIFFRACTIONr_scangle_it5.04611.4273473
X-RAY DIFFRACTIONr_scangle_other5.04911.433474
X-RAY DIFFRACTIONr_lrange_it7.26183.0855194
X-RAY DIFFRACTIONr_lrange_other7.2583.1155192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.7290.34810.3121909X-RAY DIFFRACTION100
2.729-2.8040.322970.2951847X-RAY DIFFRACTION100
2.804-2.8850.2611060.2541762X-RAY DIFFRACTION99.9465
2.885-2.9740.322870.2471737X-RAY DIFFRACTION100
2.974-3.0710.313950.2491695X-RAY DIFFRACTION100
3.071-3.1790.261020.2181601X-RAY DIFFRACTION100
3.179-3.2990.324770.2181592X-RAY DIFFRACTION100
3.299-3.4340.239630.1881536X-RAY DIFFRACTION100
3.434-3.5860.229820.1831456X-RAY DIFFRACTION100
3.586-3.7610.184810.1681399X-RAY DIFFRACTION99.8651
3.761-3.9640.186670.1661334X-RAY DIFFRACTION100
3.964-4.2040.23660.1541268X-RAY DIFFRACTION99.9251
4.204-4.4940.188530.1461206X-RAY DIFFRACTION99.9206
4.494-4.8540.183560.1481107X-RAY DIFFRACTION99.9141
4.854-5.3160.219650.1451016X-RAY DIFFRACTION100
5.316-5.9420.197590.168937X-RAY DIFFRACTION100
5.942-6.8580.143440.162845X-RAY DIFFRACTION100
6.858-8.3920.152280.148724X-RAY DIFFRACTION100
8.392-11.8360.192320.157576X-RAY DIFFRACTION100
11.836-43.060.397210.263333X-RAY DIFFRACTION95.6757

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