PDB-3ohr: Crystal structure of fructokinase from bacillus subtilis complexe...

ID or keywords:

Entry

Database: PDB / ID: 3ohr

Title

Crystal structure of fructokinase from bacillus subtilis complexed with ADP

Components

Putative fructokinase

Keywords

TRANSFERASE / metal dependent / ADP binding / D-fructose binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ROK family / Fructokinase / reductive methylation

Function / homology

Function and homology information

fructokinase / fructokinase activity / polysaccharide catabolic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.66 Å

Authors

Nocek, B. / Volkart, L. / Cuff, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.
Authors: Nocek, B. / Stein, A.J. / Jedrzejczak, R. / Cuff, M.E. / Li, H. / Volkart, L. / Joachimiak, A.

History

Deposition	Aug 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2010	Provider: repository / Type: Initial release
Supersession	Dec 1, 2010	ID: 3EPQ
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 10, 2012	Group: Database references
Revision 1.3	Mar 26, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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	3ohr.cif.gz	152.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3ohr.ent.gz	121.1 KB	Display	PDB format
PDBx/mmJSON format	3ohr.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/oh/3ohr ftp://data.pdbj.org/pub/pdb/validation_reports/oh/3ohr	HTTPS FTP

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Related structure data

Related structure data	1xc3C 3lm9C C: citing same article (ref.)
Similar structure data	6gm1-2 1goh-d 5oef-2 6gm1-1 5byr-1 5fz1-d 6pu0-d 5bys-1 1t2x-d 1xc3-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc1098

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative fructokinase

hetero molecules

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

1

A: Putative fructokinase

hetero molecules

A: Putative fructokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	112.155, 112.155, 73.716
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Putative fructokinase / Glucomannan utilization protein E Mass: 33432.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gmuE, ydhR, BSU05860 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O05510, fructokinase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H₂O
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: 4 Å³/Da / Density % sol: 69.27 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS PH 8.5 1.5 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2007 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.66→40 Å / Num. all: 62975 / Num. obs: 62904 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / R_merge(I) obs: 0.11 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.66→1.69 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2609 / % possible all: 83.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
ARP/wARP		model building
CCP4		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.66→40 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.96 / SU B: 2.565 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18567	3153	5.1 %	RANDOM
R_work	0.1636	-	-	-
all	0.18	62137	-	-
obs	0.16475	58984	98.31 %	-

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: 16.822 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.16 Å²	-0.08 Å²	0 Å²
2-	-	-0.16 Å²	0 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2273	0	33	422	2728

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	2438
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1578
X-RAY DIFFRACTION	r_angle_refined_deg	1.902	2.018	3239
X-RAY DIFFRACTION	r_angle_other_deg	1.182	3.013	3715
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.084	5	289
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.685	24.7	100
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.739	15	340
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.185	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	360
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	2530
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	450
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.909	1.5	1482
X-RAY DIFFRACTION	r_mcbond_other	0.311	1.5	595
X-RAY DIFFRACTION	r_mcangle_it	1.585	2	2315
X-RAY DIFFRACTION	r_scbond_it	2.86	3	944
X-RAY DIFFRACTION	r_scangle_it	4.433	4.5	915
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.661→1.704 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	208	-
R_work	0.292	4260	-
obs	-	-	96.5 %

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	1.5459	-0.5239	0.1516	4.6708	-0.116	0.8672	-0.0173	-0.077	-0.0089	0.184	0.0052	0.0772	-0.0397	-0.0063	0.0122	0.0856	-0.0195	-0.0234	0.1018	-0.009	0.0882	55.3584	-42.5668	-20.6234
2	1.8988	0.6052	0.4466	0.4433	-0.1745	1.4931	0.0456	-0.1411	-0.1129	0.0466	-0.0792	-0.0939	0.0319	-0.006	0.0336	0.0685	-0.0121	-0.0165	0.0964	-0.0136	0.077	58.1041	-45.1129	-15.164
3	3.711	-1.7399	3.1214	4.011	-4.0348	5.7339	-0.059	0.2668	0.2599	-0.0339	-0.0581	-0.181	-0.0738	0.2625	0.1171	0.0644	-0.0243	-0.0071	0.1058	0.0012	0.0899	61.9655	-38.3724	-27.7441
4	11.4679	6.5827	5.4025	7.7293	3.9836	3.6541	0.328	-0.0332	-0.3957	0.3119	-0.0864	-0.3886	0.3058	0.2252	-0.2416	0.0753	0.0239	-0.065	0.0957	-0.0119	0.1534	66.2239	-51.4348	-19.8472
5	1.6986	-0.5242	0.8071	0.9089	0.1226	1.0869	-0.0464	0.0184	-0.0098	0.0032	0.0667	-0.04	-0.0067	-0.0323	-0.0202	0.078	-0.0154	-0.0005	0.0807	0.0036	0.0885	47.9932	-45.9952	-29.1723
6	1.8927	1.1697	-0.3244	3.9509	-0.77	0.9216	-0.0111	0.0835	-0.0452	-0.1124	-0.011	-0.084	0.0055	0.0399	0.022	0.075	-0.0141	-0.0067	0.09	0.0069	0.0736	47.7628	-42.1307	-35.8281
7	3.9747	-2.8705	1.836	4.0267	-1.8911	2.6181	0.0286	0.2996	0.0505	-0.0902	-0.0696	-0.2397	0.1264	0.2683	0.041	0.0709	0.0045	0.0099	0.1109	-0.008	0.0878	58.7433	-47.2517	-33.5287
8	1.2447	0.2888	-0.4434	0.1195	0.0932	1.128	0.0225	-0.0741	-0.0718	0.0341	-0.0107	-0.0508	0.0931	-0.0366	-0.0117	0.0869	-0.0165	-0.0203	0.0875	0.0007	0.087	46.8689	-50.6068	-19.9411
9	1.2641	0.6742	-0.1984	2.3118	-0.2406	0.5668	0.0612	-0.1358	-0.0686	0.107	-0.0714	-0.0489	-0.0076	0.0734	0.0101	0.0762	-0.0218	-0.0052	0.0999	-0.0018	0.0693	37.7635	-49.1783	-17.1025
10	0.9218	-0.0854	-0.0697	0.9754	0.0578	0.4514	0.0542	-0.0408	0.1698	0.0305	-0.003	0.0674	-0.1029	-0.0744	-0.0511	0.0907	-0.0075	0.0143	0.094	0.0089	0.1042	29.2308	-36.815	-25.112
11	0.6746	0.1958	0.1326	1.0576	0.9899	2.3246	0.0698	0.0184	0.2616	-0.0819	-0.0191	0.0702	-0.3023	-0.0185	-0.0507	0.1362	-0.0022	0.0328	0.0735	0.0018	0.1579	32.8227	-29.4166	-25.526
12	3.6415	0.394	0.1447	7.2543	-0.4666	1.3544	0.0411	-0.3048	0.5264	0.3	-0.0132	-0.158	-0.38	0.0754	-0.0279	0.1877	-0.0337	0.0497	0.0432	-0.0781	0.1834	35.3265	-21.3676	-15.5008
13	10.1471	2.1681	-3.8606	5.7162	-1.4948	3.5637	0.339	-0.2374	0.8384	0.6506	-0.2071	0.0179	-0.301	-0.0023	-0.1319	0.2523	-0.0694	0.0483	0.1016	-0.1163	0.1883	34.6258	-23.1771	-7.4396
14	1.5435	1.09	-0.0529	4.144	0.3673	0.4885	0.0728	-0.1816	0.2191	0.2229	0.0305	0.233	-0.1136	-0.058	-0.1033	0.1316	-0.0011	0.0491	0.1077	-0.0287	0.1078	26.9813	-33.7354	-14.4979
15	0.9731	-0.0103	0.2439	0.6845	0.0776	0.5002	0.035	-0.0768	-0.064	0.0824	0.0146	-0.0026	-0.0649	0.0327	-0.0497	0.0824	-0.0213	0.0107	0.0853	-0.0102	0.0696	31.3131	-46.5457	-15.8286
16	1.291	2.1014	1.0419	3.9916	0.7536	2.4159	0.1583	-0.0215	0.0034	0.4265	-0.1541	-0.0031	-0.2143	0.2396	-0.0043	0.1968	-0.0489	-0.007	0.1567	-0.0919	0.0819	35.4716	-34.6318	-6.6876
17	5.4028	4.2702	2.1987	3.3842	1.8322	2.723	0.1743	-0.4137	0.5422	0.0685	-0.2615	0.4111	-0.4103	-0.1528	0.0872	0.2553	0.0359	0.0817	0.1778	-0.0748	0.1046	25.4884	-36.4534	-7.1592
18	1.0023	-0.4555	0.462	1.108	-0.6666	0.67	0.0732	-0.1248	0.1031	0.1777	0.02	0.057	-0.0486	-0.1121	-0.0932	0.0777	-0.0131	0.031	0.1246	-0.0017	0.0794	19.2278	-47.0642	-10.755
19	3.4271	-0.2572	-1.3338	0.3796	0.3895	0.9614	-0.0129	-0.3123	-0.045	0.1262	-0.0033	-0.0336	0.1001	0.08	0.0162	0.102	-0.023	-0.0172	0.097	0.0069	0.0499	41.0157	-47.8299	-10.8263
20	21.3899	0.1455	-3.9722	12.0278	2.4845	1.9152	-0.4087	0.6175	-1.1781	-0.0107	0.3013	-0.3315	0.6492	-0.2597	0.1075	0.5268	-0.1912	0.0161	0.1076	-0.0635	0.2691	53.8553	-61.4618	-25.6066

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 15
2	X-RAY DIFFRACTION	2	A	16 - 31
3	X-RAY DIFFRACTION	3	A	32 - 46
4	X-RAY DIFFRACTION	4	A	47 - 51
5	X-RAY DIFFRACTION	5	A	52 - 64
6	X-RAY DIFFRACTION	6	A	65 - 83
7	X-RAY DIFFRACTION	7	A	84 - 95
8	X-RAY DIFFRACTION	8	A	96 - 115
9	X-RAY DIFFRACTION	9	A	116 - 141
10	X-RAY DIFFRACTION	10	A	142 - 164
11	X-RAY DIFFRACTION	11	A	165 - 183
12	X-RAY DIFFRACTION	12	A	184 - 191
13	X-RAY DIFFRACTION	13	A	192 - 200
14	X-RAY DIFFRACTION	14	A	201 - 215
15	X-RAY DIFFRACTION	15	A	216 - 231
16	X-RAY DIFFRACTION	16	A	232 - 239
17	X-RAY DIFFRACTION	17	A	240 - 244
18	X-RAY DIFFRACTION	18	A	245 - 259
19	X-RAY DIFFRACTION	19	A	260 - 285
20	X-RAY DIFFRACTION	20	A	286 - 293

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