PDB-3p0b: Thermus thermophilus family GH57 branching enzyme: crystal struct...

ID or keywords:

Entry

Database: PDB / ID: 3p0b

Title

Thermus thermophilus family GH57 branching enzyme: crystal structure, mechanism of action and products formed

Components

TT1467 protein

Keywords

TRANSFERASE / Glycoside Hydrolase GH57 / glycogen branching

Function / homology

Function and homology information

alpha-glucan biosynthetic process /

1,4-alpha-glucan branching enzyme / 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) /

1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Pijning, T. / Dijkstra, B.W.

Citation

Journal: To be Published
Title: Thermus thermophilus GLYCOSYL HYDROLASE FAMILY 57 branching enzyme: crystal structure, mechanism of action and products formed
Authors: Palomo-Reixach, M. / Pijning, T. / Booiman, T. / Dobruchowska, J. / van der Vlist, J. / Kralj, S. / Planas, A. / Loos, K. / Kamerling, J.P. / Dijkstra, B.W. / van der Maarel, M.J.E.C. / ...

History

Deposition	Sep 28, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 20, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3p0b.cif.gz	256.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3p0b.ent.gz	205.8 KB	Display	PDB format
PDBx/mmJSON format	3p0b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/3p0b ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p0b	HTTPS FTP

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Related structure data

Related structure data	1ufaS S: Starting model for refinement
Similar structure data	5zru-1 6hfb-3 4tx2-d 5zru-2 4c0h-2 3uvv-d 5ck7-d 7ada-2 1esw-d 1ufa-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	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (3)

Deposited unit

A: TT1467 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	119.532, 119.532, 74.097
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-77- TRP

#1: Protein	TT1467 protein Mass: 61423.191 Da / Num. of mol.: 1 / Fragment: branching enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tthHB8IM / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84162, UniProt: Q5SH28*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.15 Å³/Da / Density % sol: 42.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% (w/v) PEG 3350, 8% (v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2008
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.3→40 Å / Num. all: 117389 / Num. obs: 116916 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 %
Reflection shell	Resolution: 1.3→1.35 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / Num. unique all: 16811 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UFA

1ufa

Resolution: 1.35→33 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.964 / SU B: 1.91 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18905	5862	5 %	RANDOM
R_work	0.16945	-	-	-
all	0.17	116835	-	-
obs	0.17043	110973	99.51 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 22.214 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.42 Å²	0 Å²	0 Å²
2-	-	-0.42 Å²	0 Å²
3-	-	-	0.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4124	0	6	684	4814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	4450
X-RAY DIFFRACTION	r_angle_refined_deg	1.31	1.948	6070
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.307	5	547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.404	22.165	231
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.26	15	702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.867	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	607
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	3580
X-RAY DIFFRACTION	r_mcbond_it	0.637	1.5	2652
X-RAY DIFFRACTION	r_mcangle_it	1.063	2	4252
X-RAY DIFFRACTION	r_scbond_it	1.821	3	1798
X-RAY DIFFRACTION	r_scangle_it	2.779	4.5	1816

LS refinement shell

Resolution: 1.35→1.385 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	471	-
R_work	0.254	7944	-
obs	-	-	98.38 %

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	1.0772	0.2444	-0.8065	1.9388	-1.3131	3.9309	-0.0975	-0.0188	-0.0579	0.0312	0.0756	0.1256	0.0576	-0.2247	0.0219	0.0708	0.0138	0.0452	0.0666	0.0081	0.0621	-0.2	-25.4	-22.751
2	1.1074	-0.3709	-0.303	1.3999	-0.2753	1.2677	-0.054	-0.0963	0.0166	0.1471	0.0218	-0.026	-0.1033	0.0388	0.0322	0.0892	0.0011	0.0135	0.0623	0.0069	0.0125	2.268	-15.365	-19.606
3	3.8504	-0.3419	-0.2534	2.1015	-0.3195	1.0336	0.0037	-0.0393	0.1266	0.1044	0.0074	0.1843	-0.0571	-0.1463	-0.0112	0.1111	0.0208	0.021	0.0954	0.0014	0.0666	-17.741	-2.484	-20.967
4	2.7524	-1.4402	-0.0229	1.9117	-0.1359	0.6398	-0.0314	-0.139	0.0585	0.1231	0.0349	-0.0394	-0.0098	0.0478	-0.0035	0.106	0.0061	0.0028	0.0658	0.0032	0.0021	1.974	-8.311	-18.073
5	0.8743	-0.2586	0.0637	1.6014	0.4265	2.1619	-0.0495	-0.0634	-0.1294	0.0537	0.0087	-0.0453	0.1969	0.1487	0.0407	0.1102	0.0196	0.0446	0.0647	0.0365	0.05	11.192	-32.356	-24.87
6	6.7668	2.1275	-1.2539	6.0523	-0.2239	4.711	-0.0353	-0.1291	-0.1989	0.1834	-0.0833	-0.3688	0.088	0.2296	0.1187	0.0996	0.016	0.01	0.0836	0.0284	0.032	17.542	-23.371	-21.439
7	1.1699	-0.5495	-0.2551	3.4475	-0.2227	1.0249	-0.0884	0.0761	-0.2806	-0.2575	-0.0055	0.1386	0.3177	0.1042	0.0939	0.2285	0.0235	0.0889	0.0883	0.016	0.1126	8.84	-44.51	-27.728
8	6.1437	0.6304	-1.4934	2.7539	-0.5686	2.2948	-0.275	0.0165	-0.3306	0.2069	0.0845	0.0323	0.3552	0.1256	0.1906	0.22	0.0459	0.1136	0.0812	0.0533	0.0854	7.985	-40.961	-17.483
9	3.9847	1.7857	-5.6512	17.4059	-18.3535	24.7551	-1.1616	-0.189	-0.8806	-0.7804	1.9038	1.2706	1.4807	-2.5023	-0.7421	0.7142	-0.0666	0.4568	0.4475	0.1969	0.6888	-8.933	-46.516	-13.359
10	6.288	-2.0004	-1.4028	2.7321	0.2726	1.2713	-0.3911	-0.1987	-0.5129	0.3058	0.129	0.2671	0.3635	0.0632	0.2621	0.2829	0.0498	0.1546	0.1115	0.0759	0.1464	1.43	-42.685	-10.263
11	3.8031	-1.4203	2.4038	6.3441	-2.6026	2.9179	0.1073	0.0711	-0.3926	-0.4524	0.0436	0.0735	0.1481	-0.0599	-0.151	0.2033	-0.0107	0.0811	0.1323	0.0586	0.217	-16.978	-29.658	-12.754
12	2.1339	-0.7788	0.8896	2.6591	-1.2837	3.3486	-0.0177	-0.0874	-0.1754	-0.0405	0.0889	0.298	0.1364	-0.2519	-0.0712	0.1114	0.0038	0.0482	0.1099	0.0237	0.0871	-21.451	-16.342	-17.875
13	2.9473	-2.8087	-0.0659	7.888	-1.2779	2.8632	-0.3195	-0.3396	-0.2015	0.3681	0.2886	0.3223	0.0166	-0.1105	0.0309	0.2066	0.0631	0.0895	0.1991	0.0861	0.0724	-12.456	-25.74	-1.542
14	1.3096	-0.2964	-0.196	2.9831	-2.4994	3.0716	-0.1486	-0.2995	-0.2289	0.2661	0.1573	0.1387	0.0493	-0.0683	-0.0087	0.1874	0.0449	0.0903	0.1413	0.0774	0.092	-4	-34.82	-5.988
15	2.362	-0.9853	1.0152	2.191	-1.0642	2.2892	-0.1622	-0.2778	-0.104	0.3278	0.0949	0.0288	0.0194	0.1494	0.0673	0.1769	0.0533	0.068	0.1447	0.0493	0.0395	-4.842	-23.494	-5.144
16	0.899	0.1658	-0.1379	2.6129	-0.11	3.0165	-0.2518	-0.0775	-0.2654	0.0782	0.1095	0.2399	0.4449	0.0217	0.1424	0.2016	0.0193	0.1504	0.1048	0.0632	0.1844	2.032	-42.156	-17.945
17	2.6407	0.7326	-1.3254	2.2446	-1.1322	3.2795	-0.0792	0.1948	-0.1152	-0.3976	-0.0013	0.1002	0.6546	0.0828	0.0805	0.2735	0.0488	0.0035	0.0768	-0.0269	0.0699	9.761	-37.6	-44.189
18	1.2796	-0.2779	-0.2068	1.6066	-0.6971	2.7265	0.0361	0.0513	-0.1136	-0.0612	0.0457	0.318	0.1637	-0.3205	-0.0818	0.1025	-0.0066	0.0147	0.0749	-0.0068	0.0773	0.419	-29.931	-38.98
19	1.5266	0.7658	-0.8267	1.9466	-0.8875	2.2561	-0.0267	0.1857	-0.0692	-0.2226	-0.0118	0.0384	0.1445	0.0068	0.0385	0.0988	0.0209	0.0085	0.0801	-0.0149	0.0255	8.089	-24.918	-48.365
20	1.0462	-0.6776	0.0149	3.3467	-0.5841	2.5732	-0.0365	-0.0567	-0.0729	0.0198	-0.0604	-0.2756	0.2865	0.402	0.097	0.1155	0.0418	0.0325	0.1156	0.0179	0.0516	17.48	-29.522	-35.623

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 23
2	X-RAY DIFFRACTION	2	A	24 - 80
3	X-RAY DIFFRACTION	3	A	81 - 105
4	X-RAY DIFFRACTION	4	A	106 - 129
5	X-RAY DIFFRACTION	5	A	130 - 168
6	X-RAY DIFFRACTION	6	A	169 - 175
7	X-RAY DIFFRACTION	7	A	176 - 213
8	X-RAY DIFFRACTION	8	A	214 - 226
9	X-RAY DIFFRACTION	9	A	227 - 246
10	X-RAY DIFFRACTION	10	A	247 - 273
11	X-RAY DIFFRACTION	11	A	274 - 283
12	X-RAY DIFFRACTION	12	A	284 - 323
13	X-RAY DIFFRACTION	13	A	324 - 335
14	X-RAY DIFFRACTION	14	A	336 - 358
15	X-RAY DIFFRACTION	15	A	359 - 382
16	X-RAY DIFFRACTION	16	A	383 - 415
17	X-RAY DIFFRACTION	17	A	416 - 443
18	X-RAY DIFFRACTION	18	A	444 - 476
19	X-RAY DIFFRACTION	19	A	477 - 503
20	X-RAY DIFFRACTION	20	A	504 - 517

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