PDB-9us6: Klebsiella pneumoniae maltohexaose-producing alpha-amylase, terbi...

ID or keywords:

Entry

Database: PDB / ID: 9us6

Title

Klebsiella pneumoniae maltohexaose-producing alpha-amylase, terbium derivative

Components

Maltohexaose-producing amylase

Keywords

HYDROLASE / 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

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.699 Å

Authors

Fujimoto, Z. / Kishine, N. / Momma, M.

Funding support

1items

Citation

Journal: J.Biochem. / Year: 2025
Title: Crystal structure of Klebsiella pneumoniae maltohexaose-producing alpha-amylase.
Authors: Fujimoto, Z. / Kishine, N. / Momma, M.

History

Deposition	May 1, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9us6.cif.gz	282.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9us6.ent.gz	217 KB	Display	PDB format
PDBx/mmJSON format	9us6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9us6_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9us6_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9us6_validation.xml.gz	54 KB	Display
Data in CIF	9us6_validation.cif.gz	73.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/9us6 ftp://data.pdbj.org/pub/pdb/validation_reports/us/9us6	HTTPS FTP

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Related structure data

Related structure data	9us3C 9us4C 9us5C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3) #138 - Jun 2011 Glucansucrase similarity (3)

Deposited unit

A: Maltohexaose-producing amylase

B: Maltohexaose-producing amylase

hetero molecules

149 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Maltohexaose-producing amylase

hetero molecules

defined by author
Evidence: gel filtration
74.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Maltohexaose-producing amylase

hetero molecules

defined by author
74.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.884, 107.496, 82.083
Angle α, β, γ (deg.)	90.000, 96.595, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#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
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-TB / TERBIUM(III) ION Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.64894 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.64894 Å / Relative weight: 1
Reflection	Resolution: 2.6→100 Å / Num. obs: 39283 / % possible obs: 98.6 % / Redundancy: 14.4 % / R_merge(I) obs: 0.208 / Χ²: 1.142 / Net I/σ(I): 14
Reflection shell	Resolution: 2.6→2.69 Å / R_merge(I) obs: 0.895 / Mean I/σ(I) obs: 3 / Num. unique obs: 3833 / Χ²: 0.957

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.699→46.898 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.902 / SU B: 11.56 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2195	1761	5.005 %
R_work	0.1644	33423	-
all	0.167	-	-
obs	-	35184	98.737 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.297 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.003 Å²	-0 Å²	-0.018 Å²
2-	-	0.029 Å²	0 Å²
3-	-	-	-0.021 Å²

Refinement step

Cycle: LAST / Resolution: 2.699→46.898 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10346	0	6	438	10790

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	10646
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	9593
X-RAY DIFFRACTION	r_angle_refined_deg	0.95	1.799	14443
X-RAY DIFFRACTION	r_angle_other_deg	0.361	1.773	22083
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.603	5	1297
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.147	5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.403	10	1704
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.887	10	528
X-RAY DIFFRACTION	r_chiral_restr	0.045	0.2	1464
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	12961
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2643
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	2003
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	8856
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	5070
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	5245
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	517
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.035	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.11	0.2	16
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.079	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.166	0.2	88
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.186	3.254	5200
X-RAY DIFFRACTION	r_mcbond_other	1.186	3.254	5200
X-RAY DIFFRACTION	r_mcangle_it	2.101	5.846	6493
X-RAY DIFFRACTION	r_mcangle_other	2.101	5.847	6494
X-RAY DIFFRACTION	r_scbond_it	1.062	3.319	5446
X-RAY DIFFRACTION	r_scbond_other	1.062	3.32	5447
X-RAY DIFFRACTION	r_scangle_it	1.898	6.054	7950
X-RAY DIFFRACTION	r_scangle_other	1.897	6.055	7951
X-RAY DIFFRACTION	r_lrange_it	3.598	29.733	11970
X-RAY DIFFRACTION	r_lrange_other	3.586	29.754	11950

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.699-2.769	0.312	128	0.231	2378	0.236	2626	0.954	0.973	95.4303	0.206
2.769-2.844	0.264	141	0.21	2331	0.213	2545	0.957	0.976	97.1316	0.184
2.844-2.927	0.275	134	0.211	2282	0.214	2484	0.956	0.975	97.2625	0.184
2.927-3.016	0.255	111	0.193	2231	0.196	2391	0.96	0.979	97.9507	0.167
3.016-3.115	0.25	101	0.184	2207	0.187	2342	0.963	0.979	98.5482	0.16
3.115-3.224	0.274	111	0.169	2118	0.174	2253	0.957	0.982	98.9348	0.149
3.224-3.345	0.198	86	0.157	2071	0.158	2177	0.975	0.986	99.0813	0.141
3.345-3.48	0.21	105	0.163	1994	0.165	2112	0.972	0.984	99.3845	0.148
3.48-3.634	0.204	100	0.158	1908	0.16	2020	0.979	0.987	99.4059	0.147
3.634-3.811	0.206	102	0.163	1803	0.165	1914	0.977	0.987	99.5298	0.155
3.811-4.015	0.215	94	0.147	1753	0.15	1853	0.974	0.988	99.6762	0.139
4.015-4.257	0.175	85	0.135	1642	0.137	1732	0.982	0.989	99.7113	0.13
4.257-4.548	0.206	82	0.145	1568	0.148	1653	0.975	0.988	99.8185	0.143
4.548-4.909	0.225	87	0.141	1424	0.145	1512	0.973	0.989	99.9339	0.136
4.909-5.371	0.169	64	0.139	1355	0.141	1419	0.984	0.99	100	0.133
5.371-5.995	0.229	67	0.162	1210	0.166	1277	0.973	0.987	100	0.156
5.995-6.904	0.222	50	0.164	1091	0.167	1142	0.977	0.986	99.9124	0.157
6.904-8.41	0.162	49	0.158	916	0.158	965	0.979	0.986	100	0.155
8.41-11.707	0.146	44	0.134	709	0.135	755	0.987	0.989	99.7351	0.144
11.707-46.898	0.258	20	0.22	432	0.222	454	0.956	0.972	99.5595	0.239

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