PDB-9us3: Klebsiella pneumoniae maltohexaose-producing alpha-amylase

ID or keywords:

Entry

Database: PDB / ID: 9us3

Title

Klebsiella pneumoniae maltohexaose-producing alpha-amylase

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: 1.899 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	9us3.cif.gz	294.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9us3.ent.gz	224.1 KB	Display	PDB format
PDBx/mmJSON format	9us3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9us3_validation.pdf.gz	440.4 KB	Display	wwPDB validaton report
Full document	9us3_full_validation.pdf.gz	453.1 KB	Display
Data in XML	9us3_validation.xml.gz	61.2 KB	Display
Data in CIF	9us3_validation.cif.gz	85 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/9us3 ftp://data.pdbj.org/pub/pdb/validation_reports/us/9us3	HTTPS FTP

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Related structure data

Related structure data	9us4C 9us5C 9us6C 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
74.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Maltohexaose-producing amylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.726, 107.839, 82.361
Angle α, β, γ (deg.)	90.000, 97.351, 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 23, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.899→100 Å / Num. obs: 101950 / % possible obs: 100 % / Redundancy: 7.6 % / R_merge(I) obs: 0.153 / Χ²: 0.942 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.899→1.93 Å / R_merge(I) obs: 0.842 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5084 / Χ²: 0.904

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.899→30.682 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.932 / SU B: 3.542 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2173	4923	4.984 %
R_work	0.1884	93845	-
all	0.19	-	-
obs	-	98768	96.774 %

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: 26.072 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.002 Å²	-0 Å²	0.007 Å²
2-	-	-0.01 Å²	-0 Å²
3-	-	-	0.006 Å²

Refinement step

Cycle: LAST / Resolution: 1.899→30.682 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10335	0	4	858	11197

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	10665
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	9613
X-RAY DIFFRACTION	r_angle_refined_deg	1.166	1.642	14470
X-RAY DIFFRACTION	r_angle_other_deg	1.128	1.585	22131
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.729	5	1296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.261	22.605	595
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.138	15	1711
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.23	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.04	0.2	1316
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	12324
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2652
X-RAY DIFFRACTION	r_nbd_refined	0.177	0.2	2071
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	9299
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	5075
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	4433
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	889
X-RAY DIFFRACTION	r_metal_ion_refined	0.073	0.2	18
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.221	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	97
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.111	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	0.644	2.743	5196
X-RAY DIFFRACTION	r_mcbond_other	0.644	2.742	5195
X-RAY DIFFRACTION	r_mcangle_it	1.174	4.108	6488
X-RAY DIFFRACTION	r_mcangle_other	1.174	4.109	6489
X-RAY DIFFRACTION	r_scbond_it	0.507	2.776	5469
X-RAY DIFFRACTION	r_scbond_other	0.506	2.776	5469
X-RAY DIFFRACTION	r_scangle_it	0.899	4.138	7982
X-RAY DIFFRACTION	r_scangle_other	0.899	4.138	7982
X-RAY DIFFRACTION	r_lrange_it	3.305	30.517	12564
X-RAY DIFFRACTION	r_lrange_other	3.28	30.462	12512

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.899-1.948	0.27	269	0.241	5195	X-RAY DIFFRACTION	73.0677
1.948-2.001	0.257	339	0.232	6190	X-RAY DIFFRACTION	88.5288
2.001-2.059	0.242	317	0.226	6527	X-RAY DIFFRACTION	95.9753
2.059-2.122	0.246	369	0.211	6466	X-RAY DIFFRACTION	98.6292
2.122-2.192	0.24	340	0.201	6368	X-RAY DIFFRACTION	99.8809
2.192-2.269	0.228	304	0.2	6191	X-RAY DIFFRACTION	99.9692
2.269-2.354	0.232	301	0.199	5952	X-RAY DIFFRACTION	100
2.354-2.451	0.236	297	0.193	5727	X-RAY DIFFRACTION	99.9834
2.451-2.559	0.233	289	0.192	5530	X-RAY DIFFRACTION	100
2.559-2.684	0.227	296	0.189	5238	X-RAY DIFFRACTION	100
2.684-2.829	0.215	261	0.19	5008	X-RAY DIFFRACTION	100
2.829-3.001	0.219	245	0.183	4751	X-RAY DIFFRACTION	100
3.001-3.207	0.21	250	0.179	4433	X-RAY DIFFRACTION	100
3.207-3.464	0.192	230	0.179	4159	X-RAY DIFFRACTION	100
3.464-3.794	0.217	206	0.176	3788	X-RAY DIFFRACTION	100
3.794-4.241	0.167	143	0.162	3519	X-RAY DIFFRACTION	99.9727
4.241-4.894	0.189	163	0.162	3062	X-RAY DIFFRACTION	99.969
4.894-5.989	0.21	125	0.185	2621	X-RAY DIFFRACTION	100
5.989-8.447	0.218	120	0.19	2013	X-RAY DIFFRACTION	99.9531
8.447-30.682	0.196	59	0.182	1107	X-RAY DIFFRACTION	97.005

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