PDB-4mo5: Crystal structure of AnmK bound to AMPPCP and anhMurNAc

ID or keywords:

Entry

Database: PDB / ID: 4mo5

Title

Crystal structure of AnmK bound to AMPPCP and anhMurNAc

Components

Anhydro-N-acetylmuramic acid kinase

Keywords

TRANSFERASE /

ATPase domain /

kinase /

ATP binding

Function / homology

Function and homology information

anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover /

kinase activity / carbohydrate metabolic process /

phosphorylation / response to antibiotic /

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.75 Å

Authors

Bacik, J.P. / Mark, B.L.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Conformational Itinerary of Pseudomonas aeruginosa 1,6-Anhydro-N-acetylmuramic Acid Kinase during Its Catalytic Cycle.
Authors: Bacik, J.P. / Tavassoli, M. / Patel, T.R. / McKenna, S.A. / Vocadlo, D.J. / Khajehpour, M. / Mark, B.L.

History

Deposition	Sep 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2014	Group: Database references
Revision 1.2	Mar 5, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR DETERMINED

Remark 700

SHEET DETERMINATION METHOD: AUTHOR DETERMINED

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mo5.cif.gz	554 KB	Display	PDBx/mmCIF format
PDB format	pdb4mo5.ent.gz	456.5 KB	Display	PDB format
PDBx/mmJSON format	4mo5.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/mo/4mo5 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mo5	HTTPS FTP

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Related structure data

Related structure data	4mo4C C: citing same article (ref.)
Similar structure data	4mo4-1 5ekd-d 2hz7-d 6bms-d 3btu-3 2nvw-d 1fo0-d 5vk6-d 3bts-d 1nam-d Search similar-shape structures by Omokage search (details) 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

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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: Anhydro-N-acetylmuramic acid kinase

B: Anhydro-N-acetylmuramic acid kinase

C: Anhydro-N-acetylmuramic acid kinase

D: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

1

A: Anhydro-N-acetylmuramic acid kinase

B: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

2

C: Anhydro-N-acetylmuramic acid kinase

D: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.299, 70.407, 90.968
Angle α, β, γ (deg.)	106.43, 104.43, 98.25
Int Tables number	1
Space group name H-M	P1

#1: Protein	Anhydro-N-acetylmuramic acid kinase / / AnhMurNAc kinase Mass: 40133.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I5Q5, anhydro-N-acetylmuramic acid kinase
#2: Chemical	ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid Mass: 275.255 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₇NO₇
#3: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1047 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 24% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 23, 2012
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.75→44.81 Å / Num. all: 134140 / Num. obs: 130828 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 3 % / B_iso Wilson estimate: 24.418 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.073 / Net I/σ(I): 10
Reflection shell	Resolution: 1.75→1.84 Å / Redundancy: 3 % / R_merge(I) obs: 0.493 / Mean I/σ(I) obs: 2.2 / Num. unique all: 18830 / R_sym value: 0.606 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
PHENIX		model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure: RIGID BODY REFINEMENT / Resolution: 1.75→44.806 Å / SU ML: 0.19 / σ(F): 1.96 / Phase error: 22.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2096	6689	5.11 %	RANDOM
R_work	0.1736	-	-	-
obs	0.1754	130811	97.52 %	-
all	-	130828	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→44.806 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10401	0	189	1047	11637

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10856
X-RAY DIFFRACTION	f_angle_d	1.153	14829
X-RAY DIFFRACTION	f_dihedral_angle_d	13.34	3970
X-RAY DIFFRACTION	f_chiral_restr	0.074	1665
X-RAY DIFFRACTION	f_plane_restr	0.006	1941

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.7699	0.2869	224	0.2567	4034	X-RAY DIFFRACTION	96
1.7699-1.7907	0.2895	227	0.2421	4086	X-RAY DIFFRACTION	96
1.7907-1.8126	0.2862	235	0.2392	4067	X-RAY DIFFRACTION	96
1.8126-1.8355	0.2475	220	0.2294	4035	X-RAY DIFFRACTION	96
1.8355-1.8597	0.2441	221	0.2218	4145	X-RAY DIFFRACTION	96
1.8597-1.8851	0.2582	210	0.2209	4057	X-RAY DIFFRACTION	96
1.8851-1.9121	0.2923	242	0.2097	4111	X-RAY DIFFRACTION	96
1.9121-1.9406	0.2549	214	0.206	4084	X-RAY DIFFRACTION	97
1.9406-1.9709	0.2569	223	0.2028	4140	X-RAY DIFFRACTION	97
1.9709-2.0032	0.2383	225	0.2055	4112	X-RAY DIFFRACTION	97
2.0032-2.0378	0.2522	231	0.1922	4114	X-RAY DIFFRACTION	97
2.0378-2.0748	0.2276	226	0.1861	4083	X-RAY DIFFRACTION	97
2.0748-2.1147	0.2372	203	0.1821	4154	X-RAY DIFFRACTION	97
2.1147-2.1579	0.2413	209	0.1809	4062	X-RAY DIFFRACTION	97
2.1579-2.2048	0.2122	233	0.1803	4188	X-RAY DIFFRACTION	97
2.2048-2.2561	0.2205	222	0.1788	4128	X-RAY DIFFRACTION	97
2.2561-2.3125	0.226	191	0.1699	4144	X-RAY DIFFRACTION	98
2.3125-2.3751	0.1998	257	0.1756	4150	X-RAY DIFFRACTION	98
2.3751-2.4449	0.2433	226	0.1829	4142	X-RAY DIFFRACTION	98
2.4449-2.5238	0.2287	217	0.1817	4167	X-RAY DIFFRACTION	98
2.5238-2.614	0.2286	232	0.1851	4133	X-RAY DIFFRACTION	98
2.614-2.7187	0.2292	211	0.1816	4196	X-RAY DIFFRACTION	98
2.7187-2.8424	0.2103	223	0.1772	4173	X-RAY DIFFRACTION	98
2.8424-2.9922	0.2132	204	0.1887	4181	X-RAY DIFFRACTION	98
2.9922-3.1797	0.2222	217	0.1808	4204	X-RAY DIFFRACTION	99
3.1797-3.4251	0.2103	238	0.1714	4181	X-RAY DIFFRACTION	99
3.4251-3.7696	0.1857	213	0.15	4203	X-RAY DIFFRACTION	99
3.7696-4.3147	0.1571	232	0.1371	4204	X-RAY DIFFRACTION	99
4.3147-5.4345	0.1516	222	0.1377	4231	X-RAY DIFFRACTION	99
5.4345-44.8202	0.1985	241	0.1687	4213	X-RAY DIFFRACTION	100

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	9.4649	-5.3012	3.7011	3.186	-4.6762	4.8393	-0.2927	-0.3359	0.0692	0.8072	0.2247	0.0074	-0.455	-0.1003	-0.078	0.3021	-0.0446	0.007	0.0995	-0.0456	0.2175	-6.6082	-37.5042	13.6761
2	3.3632	-0.989	0.3521	1.6388	-0.7181	1.049	0.0193	-0.0914	-0.5156	0.01	0.0105	0.2014	0.2042	-0.0413	-0.0325	0.2493	-0.0485	0.0153	0.1218	-0.0068	0.1823	-0.101	-46.4246	10.8802
3	1.6703	0.2143	-0.501	1.2158	-0.3311	0.8008	0.1281	-0.3274	0.0522	0.1664	-0.0727	-0.0117	-0.0718	0.1803	-0.0507	0.2232	-0.0741	0.0318	0.1787	-0.0266	0.1515	7.8058	-35.0117	12.1942
4	2.3062	-0.9576	0.5736	8.2154	-3.7756	6.2693	-0.2187	-0.1835	-0.1143	-0.0415	0.1968	-0.5248	0.4542	0.0561	0.0033	0.3281	0.0298	0.0864	0.2686	-0.0874	0.2708	-3.3632	-31.1038	32.4413
5	2.9222	0.4735	0.2379	7.2726	-0.5927	3.7614	-0.2908	-0.5789	-0.4581	0.6376	0.3673	-0.6345	0.8462	0.4982	-0.1062	0.5234	0.207	0.0686	0.5035	0.012	0.3294	-3.0511	-37.4864	46.1654
6	1.5234	-0.5254	-0.6702	3.6577	3.4086	9.6435	-0.2555	-0.1633	-0.0205	0.1021	0.1126	0.3109	0.3382	-0.2948	0.1072	0.2412	-0.0295	0.0982	0.2702	0.0184	0.2393	-12.1192	-28.843	33.4864
7	2.9777	1.4608	0.5793	3.4731	1.3514	2.7266	0.2484	-0.2376	0.1983	0.245	-0.0091	-0.0083	-0.2188	0.1432	-0.2393	0.1964	-0.0573	0.0522	0.1546	-0.057	0.1902	0.8278	-27.6485	10.1062
8	8.102	-4.3081	4.6662	7.8756	-3.9507	9.1153	0.1209	0.2288	0.0124	-0.3334	-0.0791	-0.2647	-0.0558	0.5419	-0.0251	0.2025	-0.0528	0.0922	0.1525	-0.0528	0.1629	20.0849	-26.0698	-11.4738
9	1.0272	-0.0364	0.1241	7.4927	-2.2843	1.7147	0.0422	-0.0854	0.0214	0.1333	-0.1248	-0.1947	-0.0598	0.171	0.0806	0.1399	-0.0465	0.0433	0.1857	-0.0314	0.1595	22.5579	-32.7902	0.5793
10	1.978	-0.1971	-1.1137	1.6379	0.6027	3.1462	0.0085	0.3015	-0.0867	-0.121	-0.0827	0.0564	0.1713	-0.0539	0.0799	0.1713	-0.0382	0.0233	0.188	-0.0332	0.1462	14.4751	-36.1025	-11.3617
11	5.2326	-1.022	0.0716	3.3886	0.3012	3.3362	-0.5231	-0.0174	-0.2453	0.6021	0.5827	-0.015	0.6126	0.9858	-0.0696	0.3979	0.1007	-0.0057	0.705	-0.1592	0.1799	29.5412	-42.6288	-20.142
12	2.448	0.4165	1.593	2.5201	1.1399	7.2095	-0.2383	-1.2697	0.1944	0.259	0.2009	-0.0364	1.0135	0.6155	0.0022	0.3333	0.184	0.0732	0.7006	-0.0528	0.3463	42.1589	-48.6964	-22.8677
13	4.7984	-2.1437	-1.2417	3.4892	0.9017	4.1221	0.0028	0.1229	-0.0296	-0.0859	0.0132	-0.1206	0.3771	0.1276	0.0009	0.2239	-0.0035	0.0397	0.2532	-0.0278	0.1312	30.8812	-41.2714	-28.7387
14	1.9963	1.424	0.5349	4.4674	1.2831	1.7704	-0.0162	0.1803	-0.0414	-0.0206	-0.111	0.1384	0.1709	-0.0839	0.1334	0.1556	-0.0234	0.013	0.1384	-0.021	0.1323	8.5159	-33.2252	-9.5557
15	6.7145	-1.2145	2.0074	2.1408	0.5146	2.61	0.0136	0.5424	0.1143	-0.3191	-0.1329	-0.1549	0.0352	0.0135	0.0898	0.2717	-0.0401	0.0875	0.1521	0.0169	0.1544	45.9915	-13.0759	-8.4984
16	2.2719	-1.257	-0.0585	4.3677	-0.425	1.2297	-0.0848	0.187	-0.0299	-0.3988	0.1068	0.0469	0.111	-0.238	-0.0209	0.188	-0.0648	0.0044	0.1845	0.0236	0.1125	34.9653	-5.6811	-5.4544
17	1.974	0.3286	-1.6242	1.1938	-0.5102	3.4011	0.0747	-0.0729	0.1903	-0.1237	0.007	-0.2181	-0.2054	0.3935	-0.0815	0.1376	-0.0031	0.0125	0.1344	0.0027	0.1898	52.5553	-1.1883	-4.7745
18	4.1376	0.7825	0.823	4.4174	-0.9777	7.4683	-0.0248	0.3109	0.6894	-0.4012	0.0863	0.4161	-0.0621	-0.3126	-0.062	0.2178	0.022	0.0076	0.2918	0.1292	0.3365	53.0931	3.9373	-35.1107
19	9.3216	5.1267	0.8214	8.6903	0.8394	8.3979	0.1708	-0.0122	0.4671	0.0692	0.0421	-0.0359	-0.2405	0.7057	-0.1898	0.1677	0.0423	0.0831	0.2279	0.0229	0.1652	63.8604	0.1801	-20.8471
20	8.2015	4.6535	-5.3798	4.712	-4.0633	8.6663	-0.0333	0.2315	-0.3436	-0.148	-0.1125	-0.493	0.5627	0.6509	0.2039	0.2936	0.0877	0.0469	0.2792	-0.0061	0.1905	63.5833	-7.1493	-19.3024
21	4.0291	3.0086	-0.2646	6.0246	0.4151	1.9875	0.0185	-0.1273	0.0852	-0.1274	0.0263	-0.1486	-0.1042	0.3056	-0.0473	0.1019	0.0092	0.0104	0.1142	0.0015	0.1179	50.8346	-4.1165	3.2503
22	2.2979	-6.0326	1.0041	10.0439	-0.7788	2.6754	0.0348	-0.3008	-0.5444	-0.0533	0.2057	1.0568	-0.185	-0.4191	-0.0332	0.1125	0.024	0.0258	0.2357	0.0459	0.3127	32.8357	3.1866	23.1787
23	1.0557	0.1217	0.6917	0.6839	-0.6184	4.4376	-0.0186	-0.0902	0.0719	0.0028	0.1068	0.1282	-0.3976	-0.2334	-0.0707	0.1181	0.0402	0.0059	0.124	-0.0006	0.2228	35.3962	7.6457	20.0215
24	0.6567	0.3698	-0.7623	1.2371	0.2009	1.2521	-0.063	0.1313	0.1372	-0.1364	0.0416	0.1588	-0.0219	-0.3346	0.0286	0.0979	0.0097	-0.0225	0.1827	0.0265	0.1475	30.6267	-2.4287	12.7325
25	4.1948	-2.3048	-0.9969	3.1969	1.5995	2.0855	-0.0462	0.1581	-0.0886	-0.169	-0.0433	0.1923	0.0112	-0.1422	0.0874	0.1209	-0.0351	-0.0049	0.2123	0.0446	0.1029	16.621	-4.1364	31.0556
26	8.9946	0.4472	3.3613	3.6599	-0.5431	2.9429	-0.2049	0.0973	0.4585	-0.1976	0.0638	-0.0559	-0.2039	0.0102	0.1121	0.1537	0.0547	-0.0053	0.1788	-0.0318	0.1859	3.3714	8.0853	34.5192
27	3.8181	2.3498	-1.6762	4.9716	-0.2709	2.2905	-0.0714	-0.1187	-0.1163	0.1451	-0.0029	-0.0354	0.1473	-0.0751	0.0734	0.1083	0.0458	-0.001	0.2051	0.0054	0.1013	16.3585	-6.64	38.1513
28	2.2452	1.8133	-0.2396	2.4318	0.9751	3.0236	-0.0958	-0.1041	-0.167	0.0437	-0.0191	-0.0508	0.2565	-0.2892	0.1081	0.1092	0.021	-0.0067	0.14	0.0326	0.1412	33.4738	-10.5223	18.567

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:26)
2	X-RAY DIFFRACTION	2	(chain A and resid 27:92)
3	X-RAY DIFFRACTION	3	(chain A and resid 93:146)
4	X-RAY DIFFRACTION	4	(chain A and resid 147:200)
5	X-RAY DIFFRACTION	5	(chain A and resid 201:282)
6	X-RAY DIFFRACTION	6	(chain A and resid 283:324)
7	X-RAY DIFFRACTION	7	(chain A and resid 325:366)
8	X-RAY DIFFRACTION	8	(chain B and resid 2:35)
9	X-RAY DIFFRACTION	9	(chain B and resid 36:108)
10	X-RAY DIFFRACTION	10	(chain B and resid 109:166)
11	X-RAY DIFFRACTION	11	(chain B and resid 167:202)
12	X-RAY DIFFRACTION	12	(chain B and resid 203:250)
13	X-RAY DIFFRACTION	13	(chain B and resid 251:323)
14	X-RAY DIFFRACTION	14	(chain B and resid 324:367)
15	X-RAY DIFFRACTION	15	(chain C and resid 2:37)
16	X-RAY DIFFRACTION	16	(chain C and resid 38:108)
17	X-RAY DIFFRACTION	17	(chain C and resid 109:183)
18	X-RAY DIFFRACTION	18	(chain C and resid 184:268)
19	X-RAY DIFFRACTION	19	(chain C and resid 269:300)
20	X-RAY DIFFRACTION	20	(chain C and resid 301:325)
21	X-RAY DIFFRACTION	21	(chain C and resid 326:364)
22	X-RAY DIFFRACTION	22	(chain D and resid 2:16)
23	X-RAY DIFFRACTION	23	(chain D and resid 17:89)
24	X-RAY DIFFRACTION	24	(chain D and resid 90:146)
25	X-RAY DIFFRACTION	25	(chain D and resid 147:200)
26	X-RAY DIFFRACTION	26	(chain D and resid 201:270)
27	X-RAY DIFFRACTION	27	(chain D and resid 271:324)
28	X-RAY DIFFRACTION	28	(chain D and resid 325:364)

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