PDB-8oqw: Crystal structure of Tannerella forsythia MurNAc kinase MurK

ID or keywords:

Entry

Database: PDB / ID: 8oqw

Title

Crystal structure of Tannerella forsythia MurNAc kinase MurK

Components

ATPase

Keywords

TRANSFERASE / sugar phosphorylation

Function / homology

: / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / ATPase

Function and homology information

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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	8oqw.cif.gz	572.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8oqw.ent.gz	363.9 KB	Display	PDB format
PDBx/mmJSON format	8oqw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8oqw_validation.pdf.gz	473.6 KB	Display	wwPDB validaton report
Full document	8oqw_full_validation.pdf.gz	484.8 KB	Display
Data in XML	8oqw_validation.xml.gz	43.1 KB	Display
Data in CIF	8oqw_validation.cif.gz	60.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oq/8oqw ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oqw	HTTPS FTP

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Related structure data

Related structure data	8oqkC 8oqxC 8ow7C 8ow9C 1x7fS C: citing same article (ref.) S: Starting model for refinement
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: ATPase

B: ATPase

C: ATPase

D: ATPase

hetero molecules

126 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATPase

B: ATPase

hetero molecules

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

2

C: ATPase

D: ATPase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.759, 59.510, 96.708
Angle α, β, γ (deg.)	74.300, 75.274, 65.953
Int Tables number	1
Space group name H-M	P1

#1: Protein	ATPase Mass: 31338.076 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0042 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.32 Å³/Da / Density % sol: 46.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2-0.3 M ammonium sulfate, 14-22% (w/v) PEG3350, bis-tris/citric acid pH 4.1-6.4 PH range: 4.1-6.4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.05→49.503 Å / Num. obs: 68635 / % possible obs: 96.1 % / Redundancy: 2.37 % / CC_1/2: 0.997 / Net I/σ(I): 9.06
Reflection shell	Resolution: 2.05→2.17 Å / Num. unique obs: 11045 / CC_1/2: 0.751

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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: 2.05→49.503 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.93 / WR_factor R_free: 0.23 / WR_factor R_work: 0.184 / SU B: 15.85 / SU ML: 0.195 / Average fsc free: 0.9454 / Average fsc work: 0.9632 / Cross valid method: FREE R-VALUE / ESU R: 0.229 / ESU R Free: 0.192
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2486	1716	2.5 %
R_work	0.2006	66914	-
all	0.202	-	-
obs	-	68630	96.216 %

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: 37.311 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.936 Å²	0.221 Å²	-1.089 Å²
2-	-	2.483 Å²	1.892 Å²
3-	-	-	-1.828 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→49.503 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8679	0	36	358	9073

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	8895
X-RAY DIFFRACTION	r_angle_refined_deg	1.126	1.636	12038
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.613	5	1120
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.515	10	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.358	10	1500
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.693	10	385
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1352
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6644
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	3727
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	6130
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	448
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.213	0.2	106
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.027	2.208	4489
X-RAY DIFFRACTION	r_mcangle_it	1.619	2.826	5606
X-RAY DIFFRACTION	r_scbond_it	1.764	2.651	4406
X-RAY DIFFRACTION	r_scangle_it	2.542	3.274	6432
X-RAY DIFFRACTION	r_lrange_it	6.131	19.914	13158

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
2.05-2.103	0.339	125	0.327	4897	0.327	5296	0.913	0.916	94.8263	0.306
2.103-2.16	0.301	124	0.303	4813	0.303	5113	0.921	0.935	96.5578	0.277
2.16-2.223	0.34	121	0.28	4716	0.281	5003	0.912	0.948	96.682	0.254
2.223-2.291	0.292	116	0.268	4535	0.269	4867	0.938	0.951	95.5619	0.241
2.291-2.366	0.288	114	0.258	4429	0.259	4700	0.949	0.958	96.6596	0.228
2.366-2.449	0.289	109	0.251	4258	0.252	4515	0.942	0.96	96.722	0.222
2.449-2.541	0.323	105	0.256	4102	0.258	4410	0.909	0.955	95.3968	0.227
2.541-2.645	0.268	101	0.232	3960	0.232	4191	0.949	0.97	96.8981	0.199
2.645-2.762	0.291	99	0.211	3845	0.213	4063	0.945	0.975	97.0711	0.181
2.762-2.896	0.238	94	0.202	3669	0.203	3864	0.962	0.977	97.3861	0.177
2.896-3.052	0.226	89	0.205	3482	0.205	3689	0.968	0.976	96.8013	0.182
3.052-3.237	0.292	84	0.187	3269	0.19	3497	0.955	0.978	95.8822	0.172
3.237-3.459	0.289	79	0.187	3078	0.189	3286	0.953	0.979	96.0743	0.175
3.459-3.735	0.186	73	0.162	2829	0.163	3047	0.979	0.985	95.2412	0.158
3.735-4.089	0.178	66	0.159	2592	0.159	2787	0.978	0.986	95.3714	0.158
4.089-4.568	0.196	62	0.153	2393	0.154	2565	0.98	0.987	95.7115	0.157
4.568-5.267	0.231	53	0.155	2069	0.156	2232	0.971	0.986	95.0717	0.164
5.267-6.433	0.251	45	0.195	1786	0.197	1900	0.963	0.978	96.3684	0.2
6.433-9.021	0.203	36	0.16	1401	0.161	1473	0.972	0.985	97.556	0.175
9.021-49.503	0.212	21	0.167	790	0.168	826	0.974	0.985	98.184	0.205

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	3.8673	-0.1078	-0.3161	3.3312	0.2941	3.69	0.0515	0.0308	0.31	-0.0275	-0.0746	-0.1467	-0.3705	0.0738	0.023	0.3771	-0.0101	0.0662	0.0669	0.0323	0.2731	13.4351	15.929	19.6279
2	3.7741	-0.9864	-0.623	4.0774	3.2097	6.7932	-0.1506	-0.2836	0.1658	0.167	0.1535	-0.1007	-0.0214	0.4586	-0.0029	0.3072	0.0036	0.0539	0.0937	0.0633	0.2417	13.3151	7.0995	21.0744
3	2.0841	1.0055	-0.4452	2.1093	-1.0185	1.6118	0.0232	0.0905	0.0628	-0.0014	-0.0271	0.008	-0.074	-0.014	0.0039	0.3	-0.0087	0.0934	0.0087	-0.0097	0.2289	27.1515	9.49	-1.4281
4	3.6505	-0.6525	-3.8446	1.7508	1.4683	7.2223	-0.0406	0.2434	0.0467	-0.1542	-0.0023	0.2301	-0.1044	-0.4996	0.0429	0.2982	-0.0271	0.0068	0.154	-0.002	0.3052	14.0953	1.0468	2.4673
5	2.9884	-1.3958	0.6198	3.5117	0.2289	3.5556	-0.1463	-0.2914	0.032	0.2102	0.1166	-0.2059	-0.0993	0.0185	0.0296	0.3858	0.0153	0.0546	0.09	-0.0169	0.3123	64.3085	31.6421	3.387
6	4.4557	-4.2131	-1.0352	7.2211	6.0903	8.3302	-0.0466	-0.031	0.0574	-0.2342	0.063	-0.035	-0.3701	0.0308	-0.0164	0.333	-0.0517	0.042	0.1015	0.0585	0.2353	62.7794	27.4025	-9.8231
7	2.3091	0.4394	-1.572	1.2129	-1.1522	3.2183	-0.0287	-0.0951	-0.1131	0.0306	-0.0176	-0.0511	0.0557	0.1574	0.0463	0.2822	-0.0473	0.0521	0.042	-0.0034	0.2336	49.5434	9.3256	-1.0011
8	3.9572	3.5122	1.1967	6.1823	1.5703	1.0146	-0.1027	0.2182	-0.2718	0.0358	0.2061	-0.4856	0.0238	0.2141	-0.1034	0.3616	0.0102	0.0929	0.1513	-0.011	0.2793	65.3299	16.0389	-10.891
9	2.2466	0.1728	-0.8458	5.8177	0.3875	2.7157	-0.0191	-0.2398	-0.3613	0.2145	-0.0536	0.0561	0.4204	0.1301	0.0727	0.4461	0.043	0.049	0.1857	0.0107	0.297	-2.5449	32.217	32.3075
10	2.4325	-1.0016	2.3212	0.9244	-1.5349	2.8791	0.0022	0.1314	-0.0155	-0.0642	0.0302	0.0642	0.0982	0.0306	-0.0324	0.3629	-0.0091	0.1042	0.1221	0.0287	0.2407	11.8035	49.2744	38.8418
11	11.7939	10.1245	-1.6645	13.1379	0.6169	1.1875	0.3784	-0.502	0.274	0.6386	-0.2134	-0.0199	0.0307	0.1323	-0.1651	0.4627	0.0641	0.0313	0.362	0.0361	0.2138	15.3939	49.9916	64.8951
12	1.9066	-0.5096	1.9491	0.4098	-0.277	2.2835	-0.0292	-0.1963	-0.0398	0.065	0.0563	0.1239	-0.1079	-0.2485	-0.0271	0.4011	0.0167	0.1348	0.125	0.0364	0.241	7.082	50.9946	44.0233
13	10.7326	1.6895	1.0217	6.4323	1.4255	6.4166	-0.1271	0.2675	0.0645	-0.397	-0.0488	0.0266	0.1178	-0.1685	0.1758	0.4267	-0.0287	0.0728	0.2228	0.0271	0.2586	55.8782	35.3406	56.1495
14	6.8455	-1.819	-0.4926	3.1525	-2.0959	3.0041	0.1919	0.0948	-0.7758	-0.5279	-0.0853	0.5162	0.6895	-0.4511	-0.1066	0.7894	-0.1336	-0.0125	0.4833	-0.0693	0.4503	47.1947	26.027	52.7667
15	1.5885	-0.3564	0.3171	5.254	-1.7904	4.4836	-0.0461	0.1301	-0.2038	-0.1843	0.1795	0.2494	0.4597	-0.315	-0.1334	0.4018	-0.0701	0.0758	0.2224	0.0238	0.2642	48.1872	32.749	63.5653
16	2.1564	-0.179	0.9669	0.9259	-0.4705	1.9393	-0.0188	0.0541	0.0674	-0.0819	-0.1244	-0.107	-0.0603	0.1756	0.1432	0.3897	0.0217	0.1245	0.1271	0.0629	0.242	36.5087	50.235	47.2991

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 81
2	X-RAY DIFFRACTION	2	ALL	A	82 - 105
3	X-RAY DIFFRACTION	3	ALL	A	106 - 249
4	X-RAY DIFFRACTION	4	ALL	A	250 - 278

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