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- PDB-9us4: Klebsiella pneumoniae maltohexaose-producing alpha-amylase in com... -

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Basic information

Entry
Database: PDB / ID: 9us4
TitleKlebsiella pneumoniae maltohexaose-producing alpha-amylase in complex with acarbose
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-acarbose / beta-acarbose / acarbose-derived trisaccharide / Maltohexaose-producing amylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: To Be 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
Revision 1.1Sep 3, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltohexaose-producing amylase
B: Maltohexaose-producing amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,05913
Polymers148,5422
Non-polymers4,51711
Water19,4741081
1
A: Maltohexaose-producing amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7717
Polymers74,2711
Non-polymers2,5006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltohexaose-producing amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2886
Polymers74,2711
Non-polymers2,0175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.913, 108.244, 82.284
Angle α, β, γ (deg.)90.000, 96.765, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Maltohexaose-producing amylase


Mass: 74270.930 Da / Num. of mol.: 2
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

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Sugars , 3 types, 7 molecules

#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: oligosaccharide / References: beta-acarbose
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 483.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: acarbose-derived trisaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 1085 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2
Details: 8% polyethylene glycol 3000, 4% polyethylene glycol 3350, 40 mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 94976 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.156 / Χ2: 0.925 / Net I/σ(I): 12
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4720 / Χ2: 0.905

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9US3

9us3


Resolution: 1.95→29.681 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.123 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2266 4624 4.998 %
Rwork0.1891 87890 -
all0.191 --
obs-92514 97.527 %
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: 26.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å2-0 Å2-0.008 Å2
2--0.013 Å2-0 Å2
3----0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10353 0 301 1081 11735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310982
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159815
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.66814942
X-RAY DIFFRACTIONr_angle_other_deg1.111.59922686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66551300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0522.584596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.697151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6291559
X-RAY DIFFRACTIONr_chiral_restr0.040.21443
X-RAY DIFFRACTIONr_chiral_restr_other0.0450.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022651
X-RAY DIFFRACTIONr_nbd_refined0.1750.22131
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.29670
X-RAY DIFFRACTIONr_nbtor_refined0.1580.25234
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.21123
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.212
X-RAY DIFFRACTIONr_nbd_other0.1610.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.233
X-RAY DIFFRACTIONr_mcbond_it0.672.7685206
X-RAY DIFFRACTIONr_mcbond_other0.672.7675205
X-RAY DIFFRACTIONr_mcangle_it1.224.1456501
X-RAY DIFFRACTIONr_mcangle_other1.224.1466502
X-RAY DIFFRACTIONr_scbond_it0.5722.8535776
X-RAY DIFFRACTIONr_scbond_other0.5722.8545777
X-RAY DIFFRACTIONr_scangle_it1.0174.2558440
X-RAY DIFFRACTIONr_scangle_other1.0174.2568441
X-RAY DIFFRACTIONr_lrange_it3.55531.04313027
X-RAY DIFFRACTIONr_lrange_other3.51630.94412944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.2843010.2595235X-RAY DIFFRACTION78.8492
2.001-2.0550.2682950.2256004X-RAY DIFFRACTION92.212
2.055-2.1150.2533390.2186047X-RAY DIFFRACTION97.155
2.115-2.180.2572990.2086095X-RAY DIFFRACTION98.9783
2.18-2.2510.2372900.1955910X-RAY DIFFRACTION99.7266
2.251-2.330.2653270.2025698X-RAY DIFFRACTION99.9668
2.33-2.4180.2352800.2015589X-RAY DIFFRACTION99.983
2.418-2.5170.2222670.1945327X-RAY DIFFRACTION99.9643
2.517-2.6290.2372750.1915089X-RAY DIFFRACTION99.9441
2.629-2.7570.2312800.1924874X-RAY DIFFRACTION99.9418
2.757-2.9060.2322290.1864674X-RAY DIFFRACTION99.9592
2.906-3.0820.2372250.194399X-RAY DIFFRACTION99.9568
3.082-3.2940.232240.1884140X-RAY DIFFRACTION99.9542
3.294-3.5580.2221750.1853902X-RAY DIFFRACTION99.951
3.558-3.8970.2061790.1713553X-RAY DIFFRACTION100
3.897-4.3550.1761600.1533227X-RAY DIFFRACTION99.8526
4.355-5.0270.1881730.1552822X-RAY DIFFRACTION100
5.027-6.1510.2051480.1872396X-RAY DIFFRACTION100
6.151-8.6740.2371010.1961872X-RAY DIFFRACTION100
8.674-29.6810.226570.1891037X-RAY DIFFRACTION96.9858

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