PDB-8oqk: Crystal structure of Tannerella forsythia sugar kinase K1058

ID or keywords:

Entry

Database: PDB / ID: 8oqk

Title

Crystal structure of Tannerella forsythia sugar kinase K1058

Components

N-acetylglucosamine kinase

Keywords

TRANSFERASE / sugar phosphorylation

Function / homology

ATPase, nucleotide binding domain / BadF/BadG/BcrA/BcrD ATPase family protein

Function and homology information

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Gogler, K. / Fink, P. / Stasiak, A.C. / Stehle, T. / Zocher, G.

Funding support

European Union,

Germany, 2items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia.
Authors: Stasiak, A.C. / Gogler, K. / Borisova, M. / Fink, P. / Mayer, C. / Stehle, T. / Zocher, G.

History

Deposition	Apr 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8oqk.cif.gz	161.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8oqk.ent.gz	97.6 KB	Display	PDB format
PDBx/mmJSON format	8oqk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oq/8oqk ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oqk	HTTPS FTP

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Related structure data

Related structure data	8oqwC 8oqxC 8ow7C 8ow9C 1x7fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: N-acetylglucosamine kinase

hetero molecules

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

1

A: N-acetylglucosamine kinase

hetero molecules

A: N-acetylglucosamine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	131.940, 131.940, 89.220
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-478- HOH

#1: Protein	N-acetylglucosamine kinase / Mass: 31898.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0034 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH1
#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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.01 Å³/Da / Density % sol: 59.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium cacodylate, MPD, PEG 8000 / PH range: 6.3 - 6.9

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 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→49.216 Å / Num. obs: 26844 / % possible obs: 100 % / Redundancy: 26.63 % / CC_1/2: 0.999 / Net I/σ(I): 19.58
Reflection shell	Resolution: 2→2.05 Å / Num. unique obs: 1946 / CC_1/2: 0.534

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X7F

1x7f

Resolution: 2→49.216 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.956 / WR_factor R_free: 0.182 / WR_factor R_work: 0.154 / SU B: 8.164 / SU ML: 0.107 / Average fsc free: 0.9644 / Average fsc work: 0.9737 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.126
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2057	1343	5.003 %
R_work	0.1771	25500	-
all	0.179	-	-
obs	-	26843	99.985 %

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: 41.513 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.277 Å²	0 Å²	-0 Å²
2-	-	-0.277 Å²	0 Å²
3-	-	-	0.555 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.216 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2183	0	10	135	2328

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2241
X-RAY DIFFRACTION	r_angle_refined_deg	1.464	1.631	3027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.335	5	276
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.699	10	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.512	10	366
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.457	10	106
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	331
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1698
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	900
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	1553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	106
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.137	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	3.594	5.777	1107
X-RAY DIFFRACTION	r_mcangle_it	4.031	7.348	1382
X-RAY DIFFRACTION	r_scbond_it	5.735	6.538	1134
X-RAY DIFFRACTION	r_scangle_it	6.887	8.046	1645
X-RAY DIFFRACTION	r_lrange_it	8.264	40.57	3307

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
2-2.052	0.277	98	0.312	1845	0.31	1943	0.941	0.937	100	0.304
2.052-2.108	0.258	95	0.263	1813	0.263	1908	0.948	0.953	100	0.244
2.108-2.169	0.291	92	0.219	1751	0.223	1843	0.947	0.968	100	0.194
2.169-2.236	0.224	91	0.206	1725	0.207	1816	0.97	0.972	100	0.18
2.236-2.309	0.234	87	0.193	1656	0.196	1744	0.964	0.975	99.9427	0.163
2.309-2.39	0.254	84	0.194	1601	0.197	1685	0.96	0.975	100	0.164
2.39-2.48	0.241	82	0.194	1560	0.196	1642	0.965	0.976	100	0.156
2.48-2.581	0.258	79	0.19	1500	0.194	1579	0.958	0.977	100	0.158
2.581-2.695	0.212	76	0.19	1434	0.191	1510	0.968	0.978	100	0.153
2.695-2.826	0.223	72	0.181	1371	0.183	1443	0.968	0.981	100	0.151
2.826-2.978	0.246	69	0.178	1316	0.181	1385	0.963	0.98	100	0.146
2.978-3.158	0.225	66	0.184	1242	0.186	1308	0.971	0.979	100	0.154
3.158-3.375	0.174	62	0.167	1179	0.167	1241	0.982	0.983	100	0.148
3.375-3.644	0.233	58	0.165	1102	0.168	1160	0.968	0.984	100	0.15
3.644-3.99	0.152	54	0.156	1026	0.156	1080	0.986	0.987	100	0.146
3.99-4.457	0.13	49	0.134	927	0.134	976	0.99	0.99	100	0.126
4.457-5.14	0.138	43	0.139	823	0.139	866	0.99	0.989	100	0.133
5.14-6.278	0.257	37	0.204	715	0.207	752	0.97	0.978	100	0.186
6.278-8.807	0.226	30	0.176	564	0.178	594	0.976	0.985	100	0.173
8.807-49.216	0.195	19	0.159	350	0.161	369	0.948	0.981	100	0.175

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	3.6468	1.9375	3.0352	5.9761	4.7409	9.4699	-0.0764	0.5226	0.0859	-0.4713	0.0859	0.0594	0.0241	0.289	-0.0095	0.2164	0.0889	-0.046	0.1893	-0.0244	0.1698	-6.0139	-20.1246	-27.5548
2	3.4627	-1.9567	0.0033	5.928	0.2148	1.4015	0.1145	0.0935	0.2183	-0.3814	-0.1134	0.5701	-0.1811	-0.4629	-0.0011	0.1601	0.0672	-0.0878	0.227	-0.0634	0.2057	-10.3679	-16.9467	-18.4911
3	1.8447	1.1973	0.1177	1.8811	0.0505	1.3104	0.0018	0.1807	-0.0803	-0.192	0.0374	-0.0152	0.0526	-0.0233	-0.0392	0.0467	0.0246	-0.0018	0.0371	-0.0033	0.0087	14.8084	-20.588	-11.2576
4	12.2295	0.1506	2.3258	1.1636	0.1867	5.6647	0.1518	0.864	-0.244	-0.497	-0.2987	0.0191	0.2439	-0.1029	0.1468	0.2675	0.1154	-0.0242	0.1711	-0.0478	0.0735	-1.8889	-28.5513	-24.3393

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 26
2	X-RAY DIFFRACTION	2	ALL	A	27 - 106
3	X-RAY DIFFRACTION	3	ALL	A	107 - 263
4	X-RAY DIFFRACTION	4	ALL	A	264 - 278

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