PDB-3amk: Structure of the Starch Branching Enzyme I (BEI) from Oryza sativa L

ID or keywords:

Entry

Database: PDB / ID: 3amk

Title

Structure of the Starch Branching Enzyme I (BEI) from Oryza sativa L

Components

Os06g0726400 protein

Keywords

TRANSFERASE / starch-branching

Function / homology

Function and homology information

starch biosynthetic process / amyloplast / cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / starch metabolic process / starch catabolic process / glycogen biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds ...
Similarity search - Function

Biological species

Oryza sativa Japonica Group (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Kakuta, Y. / Chaen, K. / Noguchi, J. / Vu, N. / Kimura, M.

Citation

Journal: Glycobiology / Year: 2011
Title: Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.
Authors: Noguchi, J. / Chaen, K. / Vu, N.T. / Akasaka, T. / Shimada, H. / Nakashima, T. / Nishi, A. / Satoh, H. / Omori, T. / Kakuta, Y. / Kimura, M.

History

Deposition	Aug 20, 2010	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3amk.cif.gz	298.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3amk.ent.gz	242.3 KB	Display	PDB format
PDBx/mmJSON format	3amk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3amk_validation.pdf.gz	451.5 KB	Display	wwPDB validaton report
Full document	3amk_full_validation.pdf.gz	458.1 KB	Display
Data in XML	3amk_validation.xml.gz	31.3 KB	Display
Data in CIF	3amk_validation.cif.gz	46.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/3amk ftp://data.pdbj.org/pub/pdb/validation_reports/am/3amk	HTTPS FTP

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Related structure data

Related structure data	3amlC C: citing same article (ref.)
Similar structure data	4hsa-1 4cce-d 4w8k-d 3aml-d 6mvt-d 4fpp-d 4yj1-d 6y6t-d 4ufi-d 6gwr-d Search similar-shape structures by Omokage search (details) 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 (5) #138 - Jun 2011 Glucansucrase similarity (5)

Deposited unit

A: Os06g0726400 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	43.894, 114.854, 66.819
Angle α, β, γ (deg.)	90.00, 93.98, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Os06g0726400 protein / Starch-branching enzyme I Mass: 81202.562 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 66-767 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Os06g0726400, SBE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0D9D0, UniProt: Q01401*PLUS
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.56 %
Crystal grow	Temperature: 293.7 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.7K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 51972 / Num. obs: 51972 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / R_merge(I) obs: 0.089 / R_sym value: 0.089 / Net I/σ(I): 13
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.611 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5175 / R_sym value: 0.611 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→28.83 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.937 / SU B: 8.391 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22056	2653	5.1 %	RANDOM
R_work	0.1806	-	-	-
obs	0.18263	49319	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 23.665 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	0 Å²	-0.03 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→28.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5502	0	46	561	6109

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	5831
X-RAY DIFFRACTION	r_angle_refined_deg	0.965	1.936	7908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.129	5	712
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.197	23.366	306
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.417	15	959
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.335	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	792
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	4577
X-RAY DIFFRACTION	r_mcbond_it	0.286	1.5	3413
X-RAY DIFFRACTION	r_mcangle_it	0.529	2	5510
X-RAY DIFFRACTION	r_scbond_it	0.843	3	2418
X-RAY DIFFRACTION	r_scangle_it	1.34	4.5	2378

LS refinement shell

Resolution: 1.897→1.947 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.311	181	-
R_work	0.288	3552	-
obs	-	-	98 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	27.1539	-8.7837	-36.2364	2.8439	11.7247	48.3624	-0.0404	1.312	-0.4341	-0.0604	-0.4896	0.1418	-0.098	-1.7315	0.53	1.1081	-0.0007	-0.0741	0.3161	0.1098	0.1275	13.1533	18.5336	-15.3104
2	1.9563	1.0808	0.4655	2.1686	0.0423	0.9058	-0.1088	0.2967	0.1265	-0.2938	0.065	0.2078	-0.1917	0.0171	0.0438	0.1139	0.018	-0.0313	0.0813	0.0034	0.0236	9.3593	3.5076	-11.4076
3	1.466	-0.1051	-0.6639	2.3402	0.3026	1.834	0.0348	0.0159	-0.1251	-0.3029	-0.0494	0.2615	0.1602	0.0199	0.0146	0.0748	0.0206	-0.0673	0.0162	-0.0414	0.1187	1.9872	-27.0629	-8.4342
4	8.7911	-0.1064	-2.4846	1.9142	0.9694	3.5583	-0.1342	-0.2711	-0.9634	0.2271	0.0213	-0.0401	0.2858	0.0691	0.1128	0.0592	0.0026	-0.0152	0.0131	0.0157	0.1904	3.2004	-24.6997	8.045
5	0.9119	-0.0208	0.6299	2.2908	0.4474	1.6972	0.0345	-0.0726	-0.0363	0.1851	-0.0311	0.1741	0.0776	-0.106	-0.0034	0.0348	-0.0145	0.043	0.0673	-0.0051	0.067	1.5407	-4.7011	17.3248
6	2.8039	1.1275	0.1483	4.0026	2.732	2.502	0.0276	-0.1969	-0.0845	0.2426	-0.1699	0.2744	0.1672	-0.1653	0.1423	0.0536	-0.0079	0.04	0.0804	0.0232	0.059	1.1575	-6.7053	23.7287
7	0.4561	-0.2258	0.0421	1.0904	0.3325	0.8827	0.0289	-0.0002	-0.0588	0.0559	-0.025	0.0301	0.0428	-0.024	-0.0039	0.0271	-0.0022	0.0199	0.066	-0.0019	0.0815	5.5357	-8.7894	13.2518
8	0.9328	-0.3697	-0.244	1.9811	0.5043	1.3456	0.0527	0.1018	-0.1108	-0.0867	-0.0307	-0.13	0.0846	0.1215	-0.0219	0.0303	0.02	0.0061	0.0886	-0.0293	0.0777	18.8908	-13.7809	-3.8408
9	0.4744	0.146	-0.0636	0.9539	0.024	0.6269	0.0115	0.0578	-0.0275	-0.1045	0.0066	-0.021	0.0008	0.0787	-0.0181	0.0326	0.0129	0.0159	0.097	-0.0098	0.051	15.343	-1.4641	-2.4204
10	1.3949	0.6017	-0.2908	0.8113	0.2316	1.3285	-0.008	0.0919	0.0418	-0.0889	-0.0222	0.053	-0.1322	-0.0517	0.0302	0.0726	0.0217	-0.0051	0.0703	-0.0069	0.0592	10.3696	8.0571	0.614
11	4.3714	0.3046	3.2667	0.2161	0.6472	3.3475	0.0193	0.3555	-0.1334	0.0126	0.0873	-0.0061	0.0353	0.3919	-0.1066	0.0793	-0.0092	0.0265	0.099	0.0043	0.0835	24.6658	7.2718	17.4226
12	0.9615	-0.2195	0.5212	1.0669	-0.2756	2.4421	0.0764	0.0293	-0.1035	-0.0399	0.0194	-0.1208	0.1681	0.2134	-0.0958	0.052	-0.0281	0.0022	0.0666	-0.0195	0.0598	24.6432	7.948	22.6542
13	0.3029	0.1857	0.0886	0.3985	0.0708	1.4887	0.0104	-0.0657	0.0406	0.0814	-0.0312	-0.0242	-0.0626	0.0212	0.0208	0.0845	-0.0178	0.0092	0.0599	-0.0075	0.066	17.9216	5.7827	31.0086
14	4.124	-2.3147	2.9659	11.2423	-5.2833	3.4502	0.4582	-0.3888	-0.9894	-0.705	-0.2032	-0.7571	0.5024	-0.1223	-0.255	0.1366	0.0764	-0.1217	0.3941	-0.0937	0.582	22.2066	-16.8491	22.3559
15	1.2437	0.6682	1.4941	0.8626	0.1854	2.6385	0.1963	-0.1166	-0.0863	0.2634	-0.052	-0.0345	0.0937	-0.0755	-0.1442	0.1492	0.0056	0.0083	0.1306	-0.0116	0.05	12.2839	-2.2241	35.1088
16	1.6361	0.6957	0.2222	1.2294	0.3132	1.5034	-0.0518	-0.0669	0.1382	0.0718	0.0844	-0.0245	-0.3016	0.0056	-0.0326	0.1319	-0.0123	0.0055	0.035	-0.0326	0.0682	16.9607	21.0839	24.8695
17	2.2635	0.3478	-0.3305	2.7426	-0.7148	1.8002	-0.0205	-0.257	0.2968	0.3275	0.016	0.0629	-0.3569	-0.0958	0.0044	0.1847	-0.0005	0.0139	0.0544	-0.0495	0.0508	15.6592	24.2905	34.6906
18	2.5256	-4.2816	1.0292	12.5323	-5.7866	5.9362	-0.115	-0.6176	0.1908	0.401	0.1309	0.2074	-0.5776	-0.1145	-0.0158	0.337	0.0581	-0.0114	0.4455	-0.1996	0.155	11.7542	24.8573	40.3239
19	11.3732	4.5951	-5.5129	3.0314	-1.1186	3.7218	0.1089	1.3249	0.9804	-0.1213	0.6651	0.1194	-0.2201	-0.4647	-0.774	0.8657	-0.074	0.0956	0.3379	0.033	0.712	16.7028	41.6721	26.7947
20	2.9107	-1.4237	1.2901	4.6273	-1.2722	3.1139	0.0058	-0.3162	0.1823	-0.0207	0.0266	0.1957	-0.5069	-0.0168	-0.0324	0.2389	-0.0425	0.0257	0.0569	-0.0591	0.094	15.2021	27.2049	31.4518

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 11
2	X-RAY DIFFRACTION	2	A	12 - 63
3	X-RAY DIFFRACTION	3	A	64 - 141
4	X-RAY DIFFRACTION	4	A	142 - 165
5	X-RAY DIFFRACTION	5	A	166 - 198
6	X-RAY DIFFRACTION	6	A	199 - 213
7	X-RAY DIFFRACTION	7	A	214 - 267
8	X-RAY DIFFRACTION	8	A	268 - 309
9	X-RAY DIFFRACTION	9	A	310 - 386
10	X-RAY DIFFRACTION	10	A	387 - 418
11	X-RAY DIFFRACTION	11	A	419 - 436
12	X-RAY DIFFRACTION	12	A	437 - 489
13	X-RAY DIFFRACTION	13	A	490 - 533
14	X-RAY DIFFRACTION	14	A	534 - 547
15	X-RAY DIFFRACTION	15	A	548 - 572
16	X-RAY DIFFRACTION	16	A	573 - 616
17	X-RAY DIFFRACTION	17	A	617 - 646
18	X-RAY DIFFRACTION	18	A	647 - 657
19	X-RAY DIFFRACTION	19	A	658 - 663
20	X-RAY DIFFRACTION	20	A	673 - 694

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