PDB-8ow7: Crystal structure of Tannerella forsythia sugar kinase K1058 in c...

ID or keywords:

Entry

Database: PDB / ID: 8ow7

Title

Crystal structure of Tannerella forsythia sugar kinase K1058 in complex with N-acetylmuramic acid (MurNAc)

Components

N-acetylglucosamine kinase

Keywords

TRANSFERASE / sugar phosphorylation

Function / homology

ATPase, nucleotide binding domain / N-acetyl-beta-muramic acid / BadF/BadG/BcrA/BcrD ATPase family protein

Function and homology information

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.06 Å

Authors

Stasiak, A.C. / Gogler, K. / Fink, P. / 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 27, 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
Revision 1.2	Nov 8, 2023	Group: Structure summary / Category: struct / Item: _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/8ow7 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8ow7	HTTPS FTP

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Related structure data

Related structure data	8oqkC 8oqwC 8oqxC 8ow9C 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

B: N-acetylglucosamine kinase

C: N-acetylglucosamine kinase

D: N-acetylglucosamine kinase

E: N-acetylglucosamine kinase

F: N-acetylglucosamine kinase

hetero molecules

201 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-acetylglucosamine kinase

C: N-acetylglucosamine kinase

hetero molecules

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

2

B: N-acetylglucosamine kinase

F: N-acetylglucosamine kinase

hetero molecules

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

3

D: N-acetylglucosamine kinase

E: N-acetylglucosamine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	143.750, 143.750, 210.950
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein

N-acetylglucosamine kinase /

Mass: 33040.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Tannerella forsythia (bacteria) / Gene: BFO_0034 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH1

#2: Sugar

ChemComp-AMU / N-acetyl-beta-muramic acid / N-acetyl-muramic acid / BETA-N-ACETYLMURAMIC ACID /

N-Acetylmuramic acid

Type: D-saccharide, beta linking / Mass: 293.270 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₈ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-SO4 / SULFATE ION /

Sulfate

Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄

Has ligand of interest

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.29	62.58
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
277	1	vapor diffusion, sitting drop	8.5	1.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol
277	2	vapor diffusion, sitting drop	8.5	1.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	2	N

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SLS	X06DA	1	1
SYNCHROTRON	SLS	X06DA	2	1

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 2M-F	1	PIXEL	Feb 5, 2022
DECTRIS PILATUS 2M-F	2	PIXEL	Feb 5, 2022

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2		1

Reflection

Entry-ID: 8OW7

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	B_iso Wilson estimate (Å²)	CC_1/2	Diffraction-ID	Net I/σ(I)
3.06-48.585	48712	100	20.38	74.28	0.99	1	7.97
3.08-48.466	47153	99.8	7.54		0.976	2	5.62

Reflection shell

Resolution (Å)	Num. unique obs	CC_1/2	Diffraction-ID
3.06-3.23	7754	0.363	1
3.08-3.27	7500	0.976	2

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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 / Resolution: 3.06→29.85 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.911 / WR_factor R_free: 0.21 / WR_factor R_work: 0.184 / SU B: 51.746 / SU ML: 0.39 / Average fsc free: 0.9449 / Average fsc work: 0.9556 / Cross valid method: FREE R-VALUE / ESU R Free: 0.405
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2454	1444	3.002 %
R_work	0.2192	46659	-
all	0.22	-	-
obs	-	48103	99.855 %

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: 86.954 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.006 Å²	0.003 Å²	0 Å²
2-	-	0.006 Å²	-0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 3.06→29.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13091	0	185	0	13276

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	13563
X-RAY DIFFRACTION	r_angle_refined_deg	0.609	1.632	18353
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.601	5	1656
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.955	10	79
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.074	10	2207
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	8.848	10	630
X-RAY DIFFRACTION	r_chiral_restr	0.046	0.2	2029
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	10212
X-RAY DIFFRACTION	r_nbd_refined	0.161	0.2	5347
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	9233
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.077	0.2	285
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.138	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.055	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.197	10.509	6642
X-RAY DIFFRACTION	r_mcangle_it	2.06	13.511	8292
X-RAY DIFFRACTION	r_scbond_it	1.267	10.947	6921
X-RAY DIFFRACTION	r_scangle_it	2.076	14.012	10061
X-RAY DIFFRACTION	r_lrange_it	5.521	68.441	19103

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
3.06-3.139	0.439	105	0.365	3390	0.368	3495	0.823	0.893	100	0.364
3.139-3.224	0.363	101	0.336	3268	0.337	3370	0.918	0.917	99.9703	0.325
3.224-3.316	0.322	99	0.309	3205	0.31	3304	0.929	0.934	100	0.292
3.316-3.417	0.308	97	0.292	3110	0.293	3207	0.931	0.939	100	0.271
3.417-3.527	0.304	93	0.283	3027	0.284	3120	0.938	0.944	100	0.259
3.527-3.649	0.242	91	0.266	2935	0.265	3026	0.956	0.953	100	0.239
3.649-3.785	0.244	88	0.254	2840	0.253	2928	0.957	0.959	100	0.227
3.785-3.937	0.236	84	0.225	2705	0.226	2789	0.966	0.967	100	0.196
3.937-4.109	0.251	81	0.212	2644	0.213	2725	0.962	0.971	100	0.186
4.109-4.305	0.231	78	0.198	2519	0.199	2597	0.966	0.975	100	0.17
4.305-4.533	0.208	74	0.176	2392	0.176	2466	0.971	0.981	100	0.153
4.533-4.801	0.207	71	0.175	2287	0.176	2358	0.974	0.98	100	0.151
4.801-5.123	0.226	66	0.175	2146	0.176	2212	0.966	0.981	100	0.152
5.123-5.52	0.214	63	0.19	2019	0.19	2082	0.975	0.976	100	0.163
5.52-6.026	0.253	57	0.213	1858	0.215	1915	0.963	0.97	100	0.181
6.026-6.703	0.291	52	0.228	1688	0.23	1740	0.945	0.966	100	0.197
6.703-7.676	0.214	48	0.196	1530	0.197	1578	0.97	0.976	100	0.175
7.676-9.25	0.166	40	0.146	1317	0.146	1357	0.985	0.987	100	0.138
9.25-12.495	0.129	33	0.138	1062	0.137	1095	0.989	0.988	100	0.14
12.495-29.85	0.37	22	0.252	717	0.255	739	0.929	0.959	100	0.256

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	2.2465	-0.9628	-0.3064	2.2852	-0.7264	1.8719	0.0613	-0.1219	-0.2073	-0.0374	-0.1405	-0.1391	0.0637	0.5462	0.0792	0.2102	-0.1083	0.0892	0.3233	0.01	0.1533	85.5463	-25.0425	-10.5289
2	2.1186	-0.1063	-0.544	2.888	0.1405	2.0247	0.0123	0.2341	0.1899	-0.088	-0.0067	-0.0186	0.0043	0.0039	-0.0056	0.1961	-0.1276	0.0119	0.2334	0.0201	0.0188	50.3266	-45.6209	8.9662
3	3.3374	0.9969	0.0462	2.4861	-0.2685	2.0052	0.1811	0.0096	-0.0117	-0.0677	0.0421	0.3128	-0.0618	-0.397	-0.2232	0.2314	-0.0156	0.0466	0.1805	0.0258	0.0789	52.2915	-17.4212	-7.7249
4	2.5381	-1.1609	0.7399	1.7073	-0.7724	3.7162	-0.4006	0.0555	0.4983	-0.2006	0.0252	0.0726	-1.4576	0.1939	0.3753	1.1008	-0.1929	-0.3215	0.3431	0.0147	0.4302	67.8848	-16.0081	41.8496
5	2.0618	-0.4745	0.326	3.3383	1.2438	2.6008	-0.0792	0.1189	0.2996	-0.3562	0.1002	-0.3042	-0.1466	1.2949	-0.0211	0.2879	-0.088	0.1002	1.0126	0.1103	0.1978	87.2469	-43.3885	34.1207
6	3.0275	-0.0243	-0.4042	1.0154	0.3136	2.5031	-0.2504	-0.003	-0.553	-0.1228	0.0776	-0.2936	0.594	0.9008	0.1728	0.5158	0.2001	0.1772	0.5268	0.0759	0.2992	77.2996	-66.2907	12.9856

Refinement TLS group

Selection: ALL

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