PDB-9ju0: C-terminally truncated dextran dextrinase bound with acarbose

ID or keywords:

Entry

Database: PDB / ID: 9ju0

Title

C-terminally truncated dextran dextrinase bound with acarbose

Components

Dextran dextrinase

Keywords

TRANSFERASE / Glucosyl transferase

Function / homology

Function and homology information

dextrin dextranase / dextrin dextranase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Gluconobacter oxydans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Tagami, T. / Matsugaki, N. / Saburi, W. / Okuyama, M. / Mori, H.

Funding support

Japan, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Structural basis of transglucosylation in dextran dextrinase, a homolog of anomer-inverting GH15 glucoside hydrolases.
Authors: Tagami, T. / Saburi, W. / Sadahiro, J. / Kumagai, Y. / Lang, W. / Matsugaki, N. / Okuyama, M. / Mori, H. / Kimura, A.

History

Deposition	Oct 7, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ju0.cif.gz	726.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ju0.ent.gz		Display	PDB format
PDBx/mmJSON format	9ju0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ju0_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9ju0_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9ju0_validation.xml.gz	143.9 KB	Display
Data in CIF	9ju0_validation.cif.gz	201.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ju/9ju0 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/9ju0	HTTPS FTP

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Related structure data

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 (4) #138 - Jun 2011 Glucansucrase similarity (1)

Deposited unit

AAA: Dextran dextrinase

BBB: Dextran dextrinase

CCC: Dextran dextrinase

DDD: Dextran dextrinase

hetero molecules

397 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Dextran dextrinase

BBB: Dextran dextrinase

hetero molecules

defined by author&software
Evidence: gel filtration
199 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: Dextran dextrinase

DDD: Dextran dextrinase

hetero molecules

defined by author&software
198 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.259, 138.969, 264.462
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Dextran dextrinase

Mass: 98111.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Gluconobacter oxydans (bacteria) / Gene: EDC20_1461 / Plasmid: pColdI / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CondonPlus(DE3)-RIL / References: UniProt: A0A0M5MSC0, dextrin dextranase

#2: Polysaccharide

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

Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose

Descriptor	Type	Program
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-c1	WURCS	PDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp4Gc]{[(4+1)][<C2O2>]{}}}	LINUCS	PDB-CARE

#3: Chemical

...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-CIT / CITRIC ACID

Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1450 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 10% PEG 6000, 6% Ethylene glycol, 100 mM sodium acetate buffer (pH 3.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
Detector	Type: RAYONIX MX225-HS / Detector: CCD / Date: Jun 6, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→49.11 Å / Num. obs: 150716 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC_1/2: 0.99 / R_rim(I) all: 0.252 / R_sym value: 0.236 / Net I/σ(I): 8.64
Reflection shell	Resolution: 2.5→2.65 Å / Redundancy: 7.6 % / Num. unique obs: 24036 / CC_1/2: 0.713 / R_rim(I) all: 1.202 / R_sym value: 1.194 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PHENIX	v1.19.1	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→49.106 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.932 / SU B: 9.48 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.413 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2109	2000	1.327 %
R_work	0.1819	148715	-
all	0.182	-	-
obs	-	150715	99.918 %

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: 34.858 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.744 Å²	-0 Å²	0 Å²
2-	-	-1.886 Å²	-0 Å²
3-	-	-	-1.859 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→49.106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26677	0	310	1450	28437

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	27593
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	23863
X-RAY DIFFRACTION	r_angle_refined_deg	1.293	1.652	37785
X-RAY DIFFRACTION	r_angle_other_deg	1.254	1.577	55033
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.084	5	3574
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.72	26.086	1349
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.908	15	3792
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.584	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	3813
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	33054
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6346
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	5768
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.171	0.2	22208
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	13812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	12574
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	1573
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.043	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.205	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.246	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.753	3.725	14311
X-RAY DIFFRACTION	r_mcbond_other	1.752	3.725	14310
X-RAY DIFFRACTION	r_mcangle_it	2.758	5.585	17880
X-RAY DIFFRACTION	r_mcangle_other	2.759	5.586	17881
X-RAY DIFFRACTION	r_scbond_it	1.839	3.82	13282
X-RAY DIFFRACTION	r_scbond_other	1.839	3.82	13283
X-RAY DIFFRACTION	r_scangle_it	2.945	5.677	19905
X-RAY DIFFRACTION	r_scangle_other	2.945	5.677	19906
X-RAY DIFFRACTION	r_lrange_it	4.365	44	31323
X-RAY DIFFRACTION	r_lrange_other	4.328	43.996	31052
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.059	0.05	29857
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	29773
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.064	0.05	29723
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.056	0.05	29917
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.054	0.05	29977
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.057	0.05	29955

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
2.5-2.565	0.292	146	0.281	10818	0.281	11046	0.78	0.804	99.2576	0.264
2.565-2.635	0.29	142	0.267	10576	0.268	10720	0.807	0.83	99.9813	0.247
2.635-2.712	0.314	139	0.254	10303	0.254	10443	0.83	0.862	99.9904	0.229
2.712-2.795	0.25	134	0.236	10042	0.236	10176	0.865	0.874	100	0.209
2.795-2.886	0.249	131	0.225	9754	0.225	9886	0.893	0.893	99.9899	0.195
2.886-2.987	0.262	127	0.214	9371	0.215	9499	0.889	0.902	99.9895	0.185
2.987-3.099	0.252	121	0.207	9081	0.208	9203	0.898	0.913	99.9891	0.178
3.099-3.225	0.233	119	0.19	8766	0.19	8887	0.918	0.936	99.9775	0.162
3.225-3.368	0.232	113	0.179	8411	0.179	8524	0.934	0.948	100	0.153
3.368-3.532	0.228	108	0.177	8048	0.178	8158	0.928	0.95	99.9755	0.155
3.532-3.722	0.202	103	0.169	7670	0.169	7773	0.95	0.959	100	0.147
3.722-3.946	0.18	98	0.159	7305	0.159	7403	0.963	0.965	100	0.139
3.946-4.216	0.177	92	0.142	6848	0.142	6940	0.969	0.973	100	0.123
4.216-4.551	0.154	86	0.132	6402	0.132	6488	0.971	0.975	100	0.115
4.551-4.982	0.131	80	0.133	5892	0.133	5972	0.978	0.978	100	0.115
4.982-5.562	0.163	72	0.153	5378	0.154	5450	0.972	0.975	100	0.132
5.562-6.409	0.212	64	0.169	4764	0.17	4828	0.962	0.97	100	0.144
6.409-7.817	0.184	55	0.151	4093	0.151	4148	0.967	0.973	100	0.131
7.817-10.917	0.157	44	0.136	3234	0.136	3278	0.973	0.977	100	0.127
10.917-49.106	0.226	26	0.22	1959	0.22	1986	0.958	0.954	99.9496	0.217

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