PDB-8oqx: Crystal structure of Tannerella forsythia MurNAc kinase MurK with...

ID or keywords:

Entry

Database: PDB / ID: 8oqx

Title

Crystal structure of Tannerella forsythia MurNAc kinase MurK with a phosphate analogue

Components

ATPase

Keywords

TRANSFERASE / sugar phosphorylation

Function / homology

ATPase, nucleotide binding domain / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER /

ATPase

Function and homology information

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 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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PDBx/mmCIF format	8oqx.cif.gz	303.8 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	8oqkC 8oqwC 8ow7C 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
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: ATPase

B: ATPase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	61.700, 55.650, 86.000
Angle α, β, γ (deg.)	90.000, 93.596, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	ATPase / Mass: 31338.076 Da / Num. of mol.: 2 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

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Non-polymers , 7 types, 225 molecules

#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₇NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.35 Å³/Da / Density % sol: 47.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.12 - 0.14 M ammonium sulfate, Citric acid + Bis/Tris propane pH=5.5, PEG 3350 (14%-18% (w/v))

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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: Aug 31, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.12→50 Å / Num. obs: 33324 / % possible obs: 100 % / Redundancy: 6.84 % / CC_1/2: 0.996 / Net I/σ(I): 10.37
Reflection shell	Resolution: 2.12→2.18 Å / Num. unique obs: 2435 / CC_1/2: 0.996

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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: 2.12→48.61 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.204 / WR_factor R_work: 0.16 / SU B: 13.904 / SU ML: 0.174 / Average fsc free: 0.956 / Average fsc work: 0.9708 / Cross valid method: FREE R-VALUE / ESU R: 0.247 / ESU R Free: 0.196
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.2351	1667	5.002 %
R_work	0.1886	31657	-
all	0.191	-	-
obs	-	33324	99.979 %

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: 33.655 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	-0 Å²	-0.295 Å²
2-	-	-0.978 Å²	-0 Å²
3-	-	-	0.828 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→48.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4333	0	127	211	4671

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	4598
X-RAY DIFFRACTION	r_angle_refined_deg	1.176	1.646	6240
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.391	5	567
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.269	10	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.469	10	749
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.958	10	191
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	704
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3363
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1891
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	3043
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	226
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.334	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	1.369	2.774	2251
X-RAY DIFFRACTION	r_mcangle_it	1.978	3.543	2811
X-RAY DIFFRACTION	r_scbond_it	3.4	3.637	2347
X-RAY DIFFRACTION	r_scangle_it	4.357	4.522	3425
X-RAY DIFFRACTION	r_lrange_it	9.355	24.043	6681

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
2.12-2.175	0.329	122	0.302	2308	0.303	2432	0.925	0.937	99.9178	0.289
2.175-2.234	0.305	120	0.27	2280	0.271	2401	0.941	0.951	99.9584	0.254
2.234-2.299	0.344	116	0.245	2197	0.25	2313	0.928	0.961	100	0.22
2.299-2.37	0.304	112	0.235	2137	0.238	2249	0.941	0.965	100	0.206
2.37-2.447	0.319	110	0.241	2095	0.245	2206	0.933	0.965	99.9547	0.207
2.447-2.533	0.268	105	0.25	1988	0.251	2093	0.955	0.962	100	0.213
2.533-2.628	0.232	100	0.222	1912	0.223	2012	0.964	0.97	100	0.191
2.628-2.735	0.241	98	0.207	1861	0.209	1959	0.961	0.975	100	0.173
2.735-2.856	0.249	96	0.204	1819	0.207	1915	0.96	0.975	100	0.172
2.856-2.995	0.259	90	0.189	1707	0.192	1797	0.96	0.979	100	0.157
2.995-3.157	0.208	86	0.175	1628	0.177	1714	0.974	0.981	100	0.149
3.157-3.347	0.215	82	0.164	1556	0.167	1638	0.976	0.984	100	0.145
3.347-3.577	0.255	76	0.173	1445	0.176	1521	0.959	0.984	100	0.157
3.577-3.862	0.202	72	0.165	1371	0.167	1443	0.974	0.986	100	0.152
3.862-4.228	0.185	66	0.148	1261	0.15	1327	0.98	0.988	100	0.137
4.228-4.722	0.157	60	0.132	1140	0.133	1200	0.988	0.99	100	0.125
4.722-5.444	0.177	53	0.144	1002	0.145	1055	0.98	0.989	100	0.135
5.444-6.647	0.268	45	0.192	862	0.195	907	0.968	0.981	100	0.174
6.647-9.314	0.242	36	0.171	686	0.175	722	0.969	0.985	100	0.165
9.314-48.61	0.23	22	0.19	402	0.192	424	0.982	0.982	100	0.201

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	4.1344	-1.2441	1.5537	2.693	0.0398	2.8183	-0.0619	-0.1593	-0.0187	0.1637	0.0927	-0.0435	-0.1538	-0.0503	-0.0308	0.155	0.0053	-0.0154	0.2669	0.0281	0.0822	-5.792	6.7604	36.1427
2	2.2763	-0.1373	-2.2789	1.9618	1.7632	9.7563	-0.0573	-0.0917	-0.0993	0.1534	0.0861	0.0189	0.0994	0.0023	-0.0288	0.1416	0.009	-0.0507	0.1875	0.0344	0.1694	-5.1383	-1.889	32.2826
3	2.6291	1.1428	-0.1359	3.3612	-0.3416	1.6099	0.0329	0.285	0.1943	-0.1054	0.0204	0.2922	0.0037	-0.0867	-0.0533	0.0342	0.0332	0.0007	0.2847	0.0108	0.1133	9.1593	11.5305	14.9634
4	7.1162	0.8304	-5.252	0.3561	-1.4098	7.818	-0.0526	0.7243	-0.2899	-0.1763	0.0696	0.1509	0.1913	-0.6315	-0.017	0.2682	-0.0062	-0.1473	0.2731	-0.0547	0.2892	-3.9572	0.669	14.5081
5	4.6149	0.8163	-0.2366	4.4642	0.1193	3.1179	-0.0247	-0.1717	0.0269	0.1491	0.0386	-0.0361	-0.12	0.0012	-0.0139	0.1761	0	-0.0923	0.2409	-0.0125	0.0977	46.8655	28.6631	30.4237
6	1.9323	-1.3063	-0.3727	1.1644	1.8258	9.0471	-0.14	0.1494	0.0716	-0.026	-0.0434	-0.0037	-0.5498	0.0889	0.1834	0.235	-0.0956	-0.0605	0.2892	0.0369	0.1731	43.9545	31.6793	16.0506
7	2.5512	1.2135	-0.2764	2.848	-0.9888	2.3137	0.0332	0.0812	-0.1245	0.0178	-0.072	-0.1018	-0.0223	0.1399	0.0388	0.0238	0.0102	-0.0272	0.2749	-0.0114	0.0348	31.4562	11.7308	15.5446
8	4.6759	3.5322	3.259	4.9509	4.054	6.1922	-0.0919	0.6638	-0.1167	-0.3617	0.2935	-0.5759	-0.2021	0.6667	-0.2016	0.1439	0.0195	0.0418	0.3791	0.0316	0.1368	45.5825	21.1164	9.353

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 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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